-For any question related to these tasks, please use the -github issue tracker -or contact - the SASC team directly at: +For any question related to Tasks, please use the +github issue tracker +or contact the SASC team directly at: + sasc@lumc.nl.
diff --git a/VERSION b/VERSION index 944880fa..03f488b0 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -3.2.0 +5.3.0 diff --git a/bam2fastx.wdl b/bam2fastx.wdl new file mode 100644 index 00000000..62827fd9 --- /dev/null +++ b/bam2fastx.wdl @@ -0,0 +1,157 @@ +version 1.0 + +# Copyright (c) 2020 Leiden University Medical Center +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. + +task Bam2Fasta { + input { + Array[File]+ bam + Array[File]+ bamIndex + String outputPrefix + Int compressionLevel = 1 + Boolean splitByBarcode = false + + String? seqIdPrefix + + String memory = "2GiB" + Int timeMinutes = 15 + String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1" + } + + command { + set -e + mkdir -p "$(dirname ~{outputPrefix})" + + # Localise the bam and pbi files so they are next to each other in the + # current folder. + bamFiles="" + for bamFile in ~{sep=" " bam} + do + ln $bamFile . + bamFiles=$bamFiles" $(basename $bamFile)" + done + + for index in ~{sep=" " bamIndex} + do + ln $index . + done + + bam2fasta \ + --output ~{outputPrefix} \ + -c ~{compressionLevel} \ + ~{true="--split-barcodes" false="" splitByBarcode} \ + ~{"--seqid-prefix " + seqIdPrefix} \ + $bamFiles + } + + output { + File fastaFile = outputPrefix + ".fasta.gz" + } + + runtime { + memory: memory + time_minutes: timeMinutes + docker: dockerImage + } + + parameter_meta { + # inputs + bam: {description: "The input pacbio bam file(s).", category: "required"} + bamIndex: {description: "The .pbi index for the input file(s).", category: "required"} + outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} + compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"} + splitByBarcode: {description: "Split output into multiple fasta files, by barcode pairs.", category: "advanced"} + seqIdPrefix: {description: "Prefix for sequence IDs in headers.", category: "advanced"} + memory: {description: "The amount of memory available to the job.", category: "advanced"} + timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"} + dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"} + + # outputs + fastaFile: {description: "The fasta output file."} + } +} + +task Bam2Fastq { + input { + Array[File]+ bam + Array[File]+ bamIndex + String outputPrefix + Int compressionLevel = 1 + Boolean splitByBarcode = false + + String? seqIdPrefix + + String memory = "2GiB" + Int timeMinutes = 15 + String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1" + } + + command { + set -e + mkdir -p "$(dirname ~{outputPrefix})" + + # Localise the bam and pbi files so they are next to each other in the + # current folder. + bamFiles="" + for bamFile in ~{sep=" " bam} + do + ln $bamFile . + bamFiles=$bamFiles" $(basename $bamFile)" + done + + for index in ~{sep=" " bamIndex} + do + ln $index . + done + + bam2fastq \ + --output ~{outputPrefix} \ + -c ~{compressionLevel} \ + ~{true="--split-barcodes" false="" splitByBarcode} \ + ~{"--seqid-prefix " + seqIdPrefix} \ + $bamFiles + } + + output { + File fastqFile = outputPrefix + ".fastq.gz" + } + + runtime { + memory: memory + time_minutes: timeMinutes + docker: dockerImage + } + + parameter_meta { + # inputs + bam: {description: "The input pacbio bam file(s).", category: "required"} + bamIndex: {description: "The .pbi index for the input file(s).", category: "required"} + outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} + compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"} + splitByBarcode: {description: "Split output into multiple fastq files, by barcode pairs.", category: "advanced"} + seqIdPrefix: {description: "Prefix for sequence IDs in headers.", category: "advanced"} + memory: {description: "The amount of memory available to the job.", category: "advanced"} + timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"} + dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"} + + # outputs + fastqFile: {description: "The fastq output file."} + } +} diff --git a/bcftools.wdl b/bcftools.wdl index 2677899b..31c7db13 100644 --- a/bcftools.wdl +++ b/bcftools.wdl @@ -1,7 +1,5 @@ version 1.0 -# MIT License -# # Copyright (c) 2018 Leiden University Medical Center # # Permission is hereby granted, free of charge, to any person obtaining a copy @@ -22,25 +20,140 @@ version 1.0 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. -task View { +task Annotate { input { + Array[String] columns = [] + Boolean force = false + Boolean keepSites = false + Boolean noVersion = false + Array[String] samples = [] + Boolean singleOverlaps = false + Array[String] removeAnns = [] File inputFile + File? inputFileIndex String outputPath = "output.vcf.gz" - String memory = "256M" - Int timeMinutes = 1 + ceil(size(inputFile, "G")) + + File? annsFile + File? annsFileIndex + String? collapse + String? exclude + File? headerLines + String? newId + String? include + String? markSites + String? regions + File? regionsFile + File? renameChrs + File? samplesFile + + Int threads = 0 + String memory = "4GiB" + Int timeMinutes = 60 + ceil(size(inputFile, "G")) String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2" - String outputType = "z" - Int compressionLevel = 1 } + Boolean compressed = basename(outputPath) != basename(outputPath, ".gz") + command { set -e mkdir -p "$(dirname ~{outputPath})" - bcftools view \ + bcftools annotate \ -o ~{outputPath} \ - -O ~{outputType} \ - -l ~{compressionLevel} \ + -O ~{true="z" false="v" compressed} \ + ~{"--annotations " + annsFile} \ + ~{"--collapse " + collapse} \ + ~{true="--columns" false="" length(columns) > 0} ~{sep="," columns} \ + ~{"--exclude " + exclude} \ + ~{true="--force" false="" force} \ + ~{"--header-lines " + headerLines} \ + ~{"--set-id " + newId} \ + ~{"--include " + include} \ + ~{true="--keep-sites" false="" keepSites} \ + ~{"--mark-sites " + markSites} \ + ~{true="--no-version" false="" noVersion} \ + ~{"--regions " + regions} \ + ~{"--regions-file " + regionsFile} \ + ~{"--rename-chrs " + renameChrs} \ + ~{true="--samples" false="" length(samples) > 0} ~{sep="," samples} \ + ~{"--samples-file " + samplesFile} \ + ~{true="--single-overlaps" false="" singleOverlaps} \ + ~{true="--remove" false="" length(removeAnns) > 0} ~{sep="," removeAnns} \ ~{inputFile} + + ~{if compressed then 'bcftools index --tbi ~{outputPath}' else ''} + } + + output { + File outputVcf = outputPath + File? outputVcfIndex = outputPath + ".tbi" + } + + runtime { + memory: memory + time_minutes: timeMinutes + docker: dockerImage + } + + parameter_meta { + # inputs + columns: {description: "Comma-separated list of columns or tags to carry over from the annotation file (see man page for details).", category: "advanced"} + force: {description: "Continue even when parsing errors, such as undefined tags, are encountered.", category: "advanced"} + keepSites: {description: "Keep sites which do not pass -i and -e expressions instead of discarding them.", category: "advanced"} + noVersion: {description: "Do not append version and command line information to the output VCF header.", category: "advanced"} + samples: {description: "List of samples for sample stats, \"-\" to include all samples.", category: "advanced"} + singleOverlaps: {description: "keep memory requirements low with very large annotation files.", category: "advanced"} + removeAnns: {description: "List of annotations to remove (see man page for details).", category: "advanced"} + inputFile: {description: "A vcf or bcf file.", category: "required"} + inputFileIndex: {description: "The index for the input vcf or bcf.", category: "common"} + outputPath: {description: "The location the output VCF file should be written.", category: "common"} + annsFile: {description: "Bgzip-compressed and tabix-indexed file with annotations (see man page for details).", category: "common"} + annsFileIndex: {description: "The index for annsFile.", category: "common"} + collapse: {description: "Treat as identical records with>>
+
+ output {
+ Int position = read_int(stdout())
+ }
+
+ runtime {
+ # 4 gigs of memory to be able to build the docker image in singularity.
+ memory: "4GiB"
+ docker: dockerImage
+ timeMinutes: 5
+ }
+
+ parameter_meta {
+ # inputs
+ sampleIds: {description: "A list of sample ids.", category: "required"}
+ sample: {description: "The sample for which the position is wanted.", category: "required"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ position: {description: ""}
+ }
}
task MapMd5 {
input {
Map[String,String] map
+ String memory = "1GiB"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
@@ -150,7 +204,7 @@ task MapMd5 {
}
runtime {
- memory: "1G"
+ memory: memory
docker: dockerImage
}
}
@@ -160,6 +214,7 @@ task StringArrayMd5 {
input {
Array[String] stringArray
+ String memory = "1GiB"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
@@ -173,7 +228,7 @@ task StringArrayMd5 {
}
runtime {
- memory: "1G"
+ memory: memory
docker: dockerImage
}
}
@@ -182,6 +237,8 @@ task TextToFile {
input {
String text
String outputFile = "out.txt"
+
+ String memory = "1GiB"
Int timeMinutes = 1
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
@@ -194,18 +251,22 @@ task TextToFile {
File out = outputFile
}
- parameter_meta {
- text: {description: "The text to print", category: "required"}
- outputFile: {description: "The name of the output file", category: "common"}
- timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
- }
runtime {
- memory: "1G"
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
+
+ parameter_meta {
+ # inputs
+ text: {description: "The text to print.", category: "required"}
+ outputFile: {description: "The name of the output file.", category: "common"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ out: {description: "File containing input text."}
+ }
}
task YamlToJson {
@@ -213,11 +274,12 @@ task YamlToJson {
File yaml
String outputJson = basename(yaml, "\.ya?ml$") + ".json"
+ String memory = "128MiB"
Int timeMinutes = 1
- String memory = "128M"
# biowdl-input-converter has python and pyyaml.
- String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
+ String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.3.0--pyhdfd78af_0"
}
+
command {
set -e
mkdir -p "$(dirname ~{outputJson})"
@@ -230,6 +292,7 @@ task YamlToJson {
json.dump(content, output_json)
CODE
}
+
output {
File json = outputJson
}
@@ -241,12 +304,15 @@ task YamlToJson {
}
parameter_meta {
+ # inputs
yaml: {description: "The YAML file to convert.", category: "required"}
outputJson: {description: "The location the output JSON file should be written to.", category: "advanced"}
memory: {description: "The maximum amount of memory the job will need.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ json: {description: "JSON file version of input YAML."}
}
}
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 7faeaff1..c695c08e 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -32,6 +32,14 @@ task Cutadapt {
Array[String] adapterRead2 = []
Array[String] frontRead2 = []
Array[String] anywhereRead2 = []
+ String reportPath = "cutadapt_report.txt"
+ # Cutadapt compresses the zipped output files with a ridiculously
+ # high compression level (5 or 6).
+ # This is not the fast compression preset. It takes up to 400% more
+ # CPU time for a 20% reduction in file size.
+ # Hence we use compression level 1 here.
+ Int compressionLevel = 1 # This only affects outputs with the .gz suffix.
+
Boolean? interleaved
String? pairFilter
Float? errorRate
@@ -52,7 +60,7 @@ task Cutadapt {
String? stripSuffix
String? prefix
String? suffix
- Int? minimumLength = 2 # Necessary to prevent creation of empty reads or 1 base reads.
+ Int? minimumLength = 2 # Necessary to prevent creation of empty reads or 1 base reads.
Int? maximumLength
Int? maxN
Boolean? discardTrimmed
@@ -73,15 +81,12 @@ task Cutadapt {
Boolean? bwa
Boolean? zeroCap
Boolean? noZeroCap
- String reportPath = "cutadapt_report.txt"
- # Cutadapt compresses the zipped output files with a ridiculously high compression level (5 or 6).
- # This is not the fast compression preset. It takes up to 400% more CPU time for a 20% reduction in file size.
- # Hence we use compression level 1 here.
- Int compressionLevel = 1 # This only affects outputs with the .gz suffix.
+ Boolean revcomp = false
+
Int cores = 4
- String memory = "~{300 + 100 * cores}M"
+ String memory = "5GiB"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 12.0 / cores)
- String dockerImage = "quay.io/biocontainers/cutadapt:2.10--py37hf01694f_1"
+ String dockerImage = "quay.io/biocontainers/cutadapt:4.4--py310h1425a21_0"
}
String realRead2output = select_first([read2output, "cut_r2.fq.gz"])
@@ -145,6 +150,7 @@ task Cutadapt {
~{true="--bwa" false="" bwa} \
~{true="--zero-cap" false="" zeroCap} \
~{true="--no-zero-cap" false="" noZeroCap} \
+ ~{if revcomp then "--revcomp" else ""} \
~{read1} \
~{read2} \
~{"> " + reportPath}
@@ -152,8 +158,8 @@ task Cutadapt {
output{
File cutRead1 = read1output
- File? cutRead2 = read2output
File report = reportPath
+ File? cutRead2 = read2output
File? tooLongOutput=tooLongOutputPath
File? tooShortOutput=tooShortOutputPath
File? untrimmedOutput=untrimmedOutputPath
@@ -173,22 +179,19 @@ task Cutadapt {
}
parameter_meta {
+ # inputs
read1: {description: "The first or single end fastq file to be run through cutadapt.", category: "required"}
read2: {description: "An optional second end fastq file to be run through cutadapt.", category: "common"}
read1output: {description: "The name of the resulting first or single end fastq file.", category: "common"}
read2output: {description: "The name of the resulting second end fastq file.", category: "common"}
- adapter: {description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.",
- category: "common"}
- front: {description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
- category: "advanced"}
- anywhere: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
- category: "advanced"}
- adapterRead2: {description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.",
- category: "common"}
- frontRead2: {description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.",
- category: "advanced"}
- anywhereRead2: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.",
- category: "advanced"}
+ adapter: {description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.", category: "common"}
+ front: {description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.", category: "advanced"}
+ anywhere: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.", category: "advanced"}
+ adapterRead2: {description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.", category: "common"}
+ frontRead2: {description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.", category: "advanced"}
+ anywhereRead2: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.", category: "advanced"}
+ reportPath: {description: "The name of the file to write cutadapts's stdout to, this contains some metrics.", category: "common"}
+ compressionLevel: {description: "The compression level if gzipped output is used.", category: "advanced"}
interleaved: {description: "Equivalent to cutadapt's --interleaved flag.", category: "advanced"}
pairFilter: {description: "Equivalent to cutadapt's --pair-filter option.", category: "advanced"}
errorRate: {description: "Equivalent to cutadapt's --error-rate option.", category: "advanced"}
@@ -230,13 +233,24 @@ task Cutadapt {
bwa: {description: "Equivalent to cutadapt's --bwa flag.", category: "advanced"}
zeroCap: {description: "Equivalent to cutadapt's --zero-cap flag.", category: "advanced"}
noZeroCap: {description: "Equivalent to cutadapt's --no-zero-cap flag.", category: "advanced"}
- reportPath: {description: "The name of the file to write cutadapts's stdout to, this contains some metrics.",
- category: "common"}
- compressionLevel: {description: "The compression level if gzipped output is used.", category: "advanced"}
+ revcomp: {description: "Equivalent to cutadapt's --revcomp flag.", category: "advanced"}
cores: {description: "The number of cores to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ cutRead1: {description: "Trimmed read one."}
+ report: {description: "Per-adapter statistics file."}
+ cutRead2: {description: "Trimmed read two in pair."}
+ tooLongOutput: {description: "Reads that are too long according to -M."}
+ tooShortOutput: {description: "Reads that are too short according to -m."}
+ untrimmedOutput: {description: "All reads without adapters (instead of the regular output file)."}
+ tooLongPairedOutput: {description: "Second reads in a pair."}
+ tooShortPairedOutput: {description: "Second reads in a pair."}
+ untrimmedPairedOutput: {description: "The second reads in a pair that were not trimmed."}
+ infoFile: {description: "Detailed information about where adapters were found in each read."}
+ restFile: {description: "The rest file."}
+ wildcardFile: {description: "The wildcard file."}
}
}
diff --git a/deconstructsigs.wdl b/deconstructsigs.wdl
new file mode 100644
index 00000000..c44bf9c0
--- /dev/null
+++ b/deconstructsigs.wdl
@@ -0,0 +1,66 @@
+# Copyright (c) 2021 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+version 1.0
+
+task DeconstructSigs {
+ input {
+ File signaturesMatrix
+ File signaturesReference
+ String outputPath = "./signatures.rds"
+
+ Int timeMinutes = 15
+ String memory = "4GiB"
+ String dockerImage = "quay.io/biocontainers/r-deconstructsigs:1.9.0--r41hdfd78af_1"
+ }
+
+ command {
+ R --no-echo << EOF
+ library(deconstructSigs)
+ tumor <- read.table("~{signaturesMatrix}", check.names=F)
+ ref <- data.frame(t(read.table("~{signaturesReference}", check.names=F, header=T, row.names="Type")), check.names=F)
+ tumor <- tumor[,colnames(ref)]
+
+ sigs <- whichSignatures(tumor.ref=tumor, row.names(tumor), signatures.ref=ref, contexts.needed=T)
+ saveRDS(sigs, "~{outputPath}")
+ EOF
+ }
+
+ output {
+ File signatureRDS = outputPath
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ signaturesMatrix: {description: "A table containing columns represtenting mutation types (matching the types in the signatures reference) and one row with the counts for each of these types for the sample of intrest.",
+ category: "required"}
+ signaturesReference: {description: "A table describing the mutational signatures, formatted like those provided by COSMIC.",
+ category: "required"}
+ outputPath: {description: "The location the output will be written to.", category: "common"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ }
+}
\ No newline at end of file
diff --git a/deepvariant.wdl b/deepvariant.wdl
new file mode 100644
index 00000000..b0ed2a19
--- /dev/null
+++ b/deepvariant.wdl
@@ -0,0 +1,109 @@
+version 1.0
+
+# Copyright (c) 2018 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task RunDeepVariant {
+ input {
+ File referenceFasta
+ File referenceFastaIndex
+ File inputBam
+ File inputBamIndex
+ String modelType
+ String outputVcf = "sample.vcf.gz"
+ String? postprocessVariantsExtraArgs
+ File? customizedModel
+ Int numShards = 8
+ String? outputGVcf
+ String? outputGVcfIndex
+ File? regions
+ String? sampleName
+ Boolean VCFStatsReport = true
+
+ # Most of the memory used is at the end, in the step where the variants
+ # are merged. This is a single-threaded high memory step. The number
+ # of shards does not influence the memory so much.
+ # The provided memory here is enough for merge human chromosome 1.
+ String memory = "48GiB"
+ Int timeMinutes = 5000
+ # Version 1.8.0 has a bug.
+ # https://github.com/google/deepvariant/issues/912
+ String dockerImage = "google/deepvariant:1.6.1"
+ }
+
+ command {
+ set -e
+ /opt/deepvariant/bin/run_deepvariant \
+ --ref ~{referenceFasta} \
+ --reads ~{inputBam} \
+ --model_type ~{modelType} \
+ --output_vcf ~{outputVcf} \
+ ~{"--output_gvcf " + outputGVcf} \
+ ~{"--customized_model " + customizedModel} \
+ ~{"--num_shards " + numShards} \
+ ~{"--regions " + regions} \
+ ~{"--sample_name " + sampleName} \
+ ~{"--postprocess_variants_extra_args " + postprocessVariantsExtraArgs} \
+ ~{true="--vcf_stats_report" false="--novcf_stats_report" VCFStatsReport}
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ cpu: numShards
+ }
+
+ output {
+ File outputVCF = outputVcf
+ File outputVCFIndex = outputVcf + ".tbi"
+ Array[File] outputVCFStatsReport = glob("*.visual_report.html")
+ File? outputGVCF = outputGVcf
+ File? outputGVCFIndex = outputGVcfIndex
+ }
+
+ parameter_meta {
+ # inputs
+ referenceFasta: {description: "Genome reference to use.", category: "required"}
+ referenceFastaIndex: {description: "Index for the genome reference file.", category: "required"}
+ inputBam: {description: "Aligned, sorted, indexed BAM file containing the reads we want to call.", category: "required"}
+ inputBamIndex: {description: "Index for the input bam file.", category: "required"}
+ modelType: {description: ". Type of model to use for variant calling. Each model_type has an associated default model, which can be overridden by the --customized_model flag.", category: "required"}
+ outputVcf: {description: "Path where we should write VCF file.", category: "required"}
+ postprocessVariantsExtraArgs: {description: "A comma-separated list of flag_name=flag_value. 'flag_name' has to be valid flags for calpostprocess_variants.py.", category: "advanced"}
+ customizedModel: {description: "A path to a model checkpoint to load for the `call_variants` step. If not set, the default for each --model_type will be used.", category: "advanced"}
+ numShards: {description: "Number of shards for make_examples step.", category: "common"}
+ outputGVcf: {description: "Path where we should write gVCF file.", category: "common"}
+ outputGVcfIndex: {description: "Path to where the gVCF index file will be written. This is needed as a workaround, set it to `outputGVcf + '.tbi.'`", category: "common"}
+ regions: {description: "List of regions we want to process, in BED/BEDPE format.", category: "advanced"}
+ sampleName: {description: "Sample name to use instead of the sample name from the input reads BAM (SM tag in the header).", category: "common"}
+ VCFStatsReport: {description: "Output a visual report (HTML) of statistics about the output VCF.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVCF: {description: "Output VCF file."}
+ outputVCFIndex: {description: "Index of output VCF file."}
+ outputVCFStatsReport: {description: "Statistics file."}
+ outputGVCF: {description: "GVCF version of VCF file(s)."}
+ outputGVCFIndex: {description: "Index of GVCF file(s)."}
+ }
+}
diff --git a/delly.wdl b/delly.wdl
index efa1bf60..b952da7e 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -1,7 +1,5 @@
version 1.0
-# MIT License
-#
# Copyright (c) 2018 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -24,15 +22,18 @@ version 1.0
task CallSV {
input {
- File bamFile
- File bamIndex
+ Array[File]+ bamFile
+ Array[File]+ bamIndex
File referenceFasta
File referenceFastaFai
- String outputPath = "./delly/delly.vcf"
+ String outputPath = "./delly/delly.bcf"
- String memory = "15G"
- Int timeMinutes = 300
- String dockerImage = "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
+ File? genotypeBcf
+ File? genotypeBcfIndex
+
+ String memory = "15GiB"
+ Int timeMinutes = 600
+ String dockerImage = "quay.io/biocontainers/delly:1.1.6--ha41ced6_0"
}
command {
@@ -41,11 +42,13 @@ task CallSV {
delly call \
-o ~{outputPath} \
-g ~{referenceFasta} \
- ~{bamFile}
+ ~{"-v " + genotypeBcf} \
+ ~{sep=" " bamFile}
}
output {
File dellyBcf = outputPath
+ File dellyBcfIndex = outputPath + ".csi"
}
runtime {
@@ -56,13 +59,68 @@ task CallSV {
parameter_meta {
# inputs
- bamFile: {description: "The bam file to process.", category: "required"}
- bamIndex: {description: "The index bam file.", category: "required"}
+ bamFile: {description: "The bam files to process.", category: "required"}
+ bamIndex: {description: "The indexes for the bam files.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
- referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
- outputPath: {description: "The location the output VCF file should be written.", category: "common"}
- memory: {description: "The memory required to run the programs", category: "advanced"}
+ referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
+ outputPath: {description: "The location the output BCF file should be written.", category: "common"}
+ genotypeBcf: {description: "A BCF with SVs to get genotyped in the samples.", category: "advanced"}
+ genotypeBcfIndex: {description: "The index for the genotype BCF file.", category: "advanced"}
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ dellyBcf: {description: "File containing structural variants."}
}
}
+
+
+task SomaticFilter {
+ input {
+ File dellyBcf
+ File dellyBcfIndex
+ Array[String]+ normalSamples
+ Array[String]+ tumorSamples
+ String outputPath = "./delly/delly_filter.bcf"
+
+ String memory = "15GiB"
+ Int timeMinutes = 300
+ String dockerImage = "quay.io/biocontainers/delly:1.1.6--ha41ced6_0"
+ }
+
+ command <<<
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ for SAMPLE in ~{sep=" " normalSamples}; do echo -e "${SAMPLE}\tcontrol" >> samples.tsv; done
+ for SAMPLE in ~{sep=" " tumorSamples}; do echo -e "${SAMPLE}\ttumor" >> samples.tsv; done
+
+ delly filter \
+ -f somatic \
+ -o ~{outputPath} \
+ -s samples.tsv \
+ ~{dellyBcf}
+ >>>
+
+ output {
+ File filterBcf = outputPath
+ File filterBcfIndex = outputPath + ".csi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ dellyBcf: {description: "The BCF file produced by delly.", category: "required"}
+ dellyBcfIndex: {description: "The index for the delly BCF file.", category: "required"}
+ normalSamples: {description: "The names for the normal samples as used in the delly BCF file.", category: "required"}
+ tumorSamples: {description: "The names for the tumor samples as used in the delly BCF file.", category: "required"}
+ outputPath: {description: "The location the output BCF file should be written.", category: "common"}
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ }
+}
\ No newline at end of file
diff --git a/duphold.wdl b/duphold.wdl
new file mode 100644
index 00000000..0426da56
--- /dev/null
+++ b/duphold.wdl
@@ -0,0 +1,75 @@
+version 1.0
+
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Duphold {
+ input {
+ File inputVcf
+ File bamFile
+ File bamIndex
+ File referenceFasta
+ File referenceFastaFai
+ String sample
+ String outputPath = "./duphold.vcf"
+
+ String memory = "15GiB"
+ Int timeMinutes = 1440
+ String dockerImage = "quay.io/biocontainers/duphold:0.2.1--h516909a_1"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ export DUPHOLD_SAMPLE_NAME=~{sample}
+ duphold \
+ -v ~{inputVcf} \
+ -b ~{bamFile} \
+ -f ~{referenceFasta} \
+ -o ~{outputPath}
+ }
+
+ output {
+ File outputVcf = outputPath
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputVcf: {description: "The VCF file to process.", category: "required"}
+ bamFile: {description: "The bam file to process.", category: "required"}
+ bamIndex: {description: "The index of the bam file.", category: "required"}
+ referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
+ referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
+ sample: {description: "The name of the sample.", category: "required"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
+ timeMinutes: {description: "The maximum duration (in minutes) the tool is allowed to run.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "Duphold annotated VCF file."}
+ }
+}
diff --git a/extractSigPredictHRD.wdl b/extractSigPredictHRD.wdl
new file mode 100644
index 00000000..1520b608
--- /dev/null
+++ b/extractSigPredictHRD.wdl
@@ -0,0 +1,71 @@
+version 1.0
+
+# Copyright (c) 2021 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task ExtractSigPredictHRD {
+ input {
+ String outputDir = "."
+ String sampleName
+ File snvIndelVcf
+ File snvIndelVcfIndex
+ File svVcf
+ File svVcfIndex
+ Boolean hg38 = false
+
+ String memory = "3GiB"
+ Int timeMinutes = 10
+ String dockerImage = "quay.io/biowdl/chord-mutsigextractor:2.00_1.14"
+ }
+
+ command {
+ extractSigPredictHRD.R \
+ ~{outputDir} \
+ ~{sampleName} \
+ ~{snvIndelVcf} \
+ ~{svVcf} \
+ ~{if hg38 then "RG_38" else "RG_37"}
+ }
+
+ output {
+ File chordPrediction = "~{outputDir}/~{sampleName}_chord_prediction.txt"
+ File chordSignatures = "~{outputDir}/~{sampleName}_chord_signatures.txt"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ outputDir: {description: "The directory the outout will be written to.", category: "required"}
+ sampleName: {description: "The name of the sample.", category: "required"}
+ snvIndelVcf: {description: "A VCF file with SNVs and indels.", category: "required"}
+ snvIndelVcfIndex: {description: "The index for the SNV/indel VCF file.", category: "required"}
+ svVcf: {description: "A VCF file with SVs.", category: "required"}
+ svVcfIndex: {description: "The index for the SV VCF file.", category: "required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
\ No newline at end of file
diff --git a/fastp.wdl b/fastp.wdl
new file mode 100644
index 00000000..9849738b
--- /dev/null
+++ b/fastp.wdl
@@ -0,0 +1,124 @@
+version 1.0
+
+# MIT License
+#
+# Copyright (c) 2022 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Fastp {
+ input {
+ File read1
+ File read2
+ String outputPathR1
+ String outputPathR2
+ String htmlPath
+ String jsonPath
+
+ Int compressionLevel = 1
+ Boolean correction = false
+ Int lengthRequired = 15
+ Int? split
+ Boolean performAdapterTrimming = true
+ Boolean performQualityFiltering = true
+ Boolean performLengthFiltering = true
+ Boolean? performPolyGTrimming
+
+ Int threads = 4
+ String memory = "50GiB"
+ Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 6.0 / threads)
+ String dockerImage = "quay.io/biocontainers/fastp:0.23.2--h5f740d0_3"
+
+ Int? noneInt
+ }
+
+ String outputDirR1 = sub(outputPathR1, basename(outputPathR1), "")
+ String outputDirR2 = sub(outputPathR2, basename(outputPathR2), "")
+
+ String polyGTrimmingFlag = if defined(performPolyGTrimming)
+ then
+ if select_first([performPolyGTrimming]) then "--trim_poly_g" else "--disable_trim_poly_g"
+ else ""
+
+ Int? effectiveSplit = if select_first([split, 1]) > 1 then split else noneInt
+
+ command <<<
+ set -e
+ mkdir -p $(dirname ~{outputPathR1})
+ mkdir -p $(dirname ~{outputPathR2})
+ mkdir -p $(dirname ~{htmlPath})
+ mkdir -p $(dirname ~{jsonPath})
+
+ # predict output paths
+ seq 1 ~{if defined(effectiveSplit) then effectiveSplit else "2"} | awk '{print "~{outputDirR1}/"$0".~{basename(outputPathR1)}"}' > r1_paths
+ seq 1 ~{if defined(effectiveSplit) then effectiveSplit else "2"} | awk '{print "~{outputDirR2}/"$0".~{basename(outputPathR2)}"}' > r2_paths
+ fastp \
+ -i ~{read1} \
+ ~{"-I " + read2} \
+ -o ~{outputPathR1} \
+ ~{"-O " + outputPathR2} \
+ -h ~{htmlPath} \
+ -j ~{jsonPath} \
+ -z ~{compressionLevel} \
+ ~{if correction then "--correction" else ""} \
+ --length_required ~{lengthRequired} \
+ --thread ~{select_first([effectiveSplit, threads])} \
+ ~{"--split " + effectiveSplit} \
+ ~{if defined(effectiveSplit) then "-d 0" else ""} \
+ ~{if performAdapterTrimming then "" else "--disable_adapter_trimming"} \
+ ~{if performQualityFiltering then "" else "--disable_quality_filtering"} \
+ ~{if performLengthFiltering then "" else "--disable_length_filtering"} \
+ ~{polyGTrimmingFlag}
+ >>>
+
+ output {
+ File htmlReport = htmlPath
+ File jsonReport = jsonPath
+ Array[File] clippedR1 = if defined(effectiveSplit) then read_lines("r1_paths") else [outputPathR1]
+ Array[File] clippedR2 = if defined(effectiveSplit) then read_lines("r2_paths") else [outputPathR2]
+ }
+
+ runtime {
+ cpu: select_first([effectiveSplit, threads])
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ read1: {description: "The R1 fastq file.", category: "required"}
+ read2: {description: "The R2 fastq file.", category: "required"}
+ outputPathR1: {description: "The output path for the R1 file.", category: "required"}
+ outputPathR2: {description: "The output path for the R2 file.", category: "required"}
+ htmlPath: {description: "The path to write the html report to.", category: "required"}
+ jsonPath: {description: "The path to write the json report to.", category: "required"}
+ compressionLevel: {description: "The compression level to use for the output.", category: "advanced"}
+ correction: {description: "Whether or not to apply overlap based correction.", category: "advanced"}
+ lengthRequired: {description: "The minimum read length.", category: "advanced"}
+ split: {description: "The number of chunks to split the files into. Number of threads will be set equal to the amount of splits.", category: "common"}
+ performAdapterTrimming: {description: "Whether adapter trimming should be performed or not.", category: "advanced"}
+ performQualityFiltering: {description: "Whether reads should be filtered based on quality scores.", category: "advanced"}
+ performLengthFiltering: {description: "Whether reads shoulde be filtered based on lengths.", catgegory: "advanced"}
+ performPolyGTrimming: {description: "Whether or not poly-G-tail trimming should be performed. If undefined fastp's default behaviour will be used, ie. enabled for NextSeq/NovaSeq data as detected from read headers.", category: "advanced"}
+ threads: {description: "The number of threads to use. Only used if the split input is not set.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ }
+}
\ No newline at end of file
diff --git a/fastqFilter.wdl b/fastqFilter.wdl
new file mode 100644
index 00000000..3701b8aa
--- /dev/null
+++ b/fastqFilter.wdl
@@ -0,0 +1,66 @@
+version 1.0
+
+# MIT License
+#
+# Copyright (c) 2023 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task FastqFilter {
+ input {
+ Array[File]+ fastq
+ Array[String]+ outputPaths
+ Int? minLength
+ Int? maxLength
+
+ String memory = "1GiB"
+ Int timeMinutes = 1 + ceil(size(fastq, "G"))
+ String dockerImage = "quay.io/biocontainers/fastq-filter:0.3.0--py39hf95cd2a_1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{sep=" " outputPaths})
+ fastq-filter \
+ -o ~{sep=" -o " outputPaths} \
+ ~{"-l " + minLength} \
+ ~{"-L " + maxLength} \
+ ~{sep=" " fastq}
+ }
+
+ output {
+ Array[File] filtered = outputPaths
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ fastq: {description: "A list of fastq files to filter.", category: "required"}
+ outputPaths: {description: "A list containing the output paths for each input fastq file.", category: "required"}
+ minLength: {description: "Equivalent to fastq-filter's `--min-length` option.", category: "common"}
+ maxLength: {description: "Equivalent to fastq-filter's `--max-length` option.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ }
+}
\ No newline at end of file
diff --git a/fastqc.wdl b/fastqc.wdl
index 04b6813f..da31882c 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -29,6 +29,7 @@ task Fastqc {
Boolean noFilter = false
Boolean extract = false
Boolean nogroup = false
+
Int? minLength
String? format
File? contaminants
@@ -37,33 +38,36 @@ task Fastqc {
Int? kmers
String? dir
- Int threads = 1
# Set javaXmx a little high. Equal to fastqc default with 7 threads.
# This is because some fastq files need more memory. 2G per core
# is a nice cluster default, so we use all the rest of the memory for
# fastqc so we should have as little OOM crashes as possible even with
# weird edge case fastq's.
- String javaXmx="1750M"
- String memory = "2G"
+ String javaXmx="1750M"
+ Int threads = 1
+ String memory = "2GiB"
Int timeMinutes = 1 + ceil(size(seqFile, "G")) * 4
- String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0"
- Array[File]? NoneArray
- File? NoneFile
+ String dockerImage = "quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
+
+ Array[File]? noneArray
+ File? noneFile
}
# Chops of the .gz extension if present.
- # The Basename needs to be taken here. Otherwise paths might differ between similar jobs.
+ # The Basename needs to be taken here. Otherwise paths might differ
+ # between similar jobs.
String name = basename(sub(seqFile, "\.gz$",""))
- # This regex chops of the extension and replaces it with _fastqc for the reportdir.
+ # This regex chops of the extension and replaces it with _fastqc for
+ # the reportdir.
# Just as fastqc does it.
String reportDir = outdirPath + "/" + sub(name, "\.[^\.]*$", "_fastqc")
- # We reimplement the perl wrapper here. This has the advantage that it gives
- # us more control over the amount of memory used.
+ # We reimplement the perl wrapper here. This has the advantage that it
+ # gives us more control over the amount of memory used.
command <<<
set -e
- mkdir -p ~{outdirPath}
- FASTQC_DIR="/usr/local/opt/fastqc-0.11.9"
+ mkdir -p "~{outdirPath}"
+ FASTQC_DIR="/usr/local/opt/fastqc-0.12.1"
export CLASSPATH="$FASTQC_DIR:$FASTQC_DIR/sam-1.103.jar:$FASTQC_DIR/jbzip2-0.9.jar:$FASTQC_DIR/cisd-jhdf5.jar"
java -Djava.awt.headless=true -XX:ParallelGCThreads=1 \
-Xms200M -Xmx~{javaXmx} \
@@ -86,23 +90,24 @@ task Fastqc {
>>>
output {
- File? rawReport = if extract then reportDir + "/fastqc_data.txt" else NoneFile
File htmlReport = reportDir + ".html"
File reportZip = reportDir + ".zip"
- File? summary = if extract then reportDir + "/summary.txt" else NoneFile
- Array[File]? images = if extract then glob(reportDir + "/Images/*.png") else NoneArray
+ File? summary = if extract then reportDir + "/summary.txt" else noneFile
+ File? rawReport = if extract then reportDir + "/fastqc_data.txt" else noneFile
+ Array[File]? images = if extract then glob(reportDir + "/Images/*.png") else noneArray
}
runtime {
cpu: threads
memory: memory
- docker: dockerImage
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
seqFile: {description: "A fastq file.", category: "required"}
- outdirPath: {description: "The path to write the output to", catgory: "required"}
+ outdirPath: {description: "The path to write the output to.", catgory: "required"}
casava: {description: "Equivalent to fastqc's --casava flag.", category: "advanced"}
nano: {description: "Equivalent to fastqc's --nano flag.", category: "advanced"}
noFilter: {description: "Equivalent to fastqc's --nofilter flag.", category: "advanced"}
@@ -115,24 +120,30 @@ task Fastqc {
limits: {description: "Equivalent to fastqc's --limits option.", category: "advanced"}
kmers: {description: "Equivalent to fastqc's --kmers option.", category: "advanced"}
dir: {description: "Equivalent to fastqc's --dir option.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
threads: {description: "The number of cores to use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ htmlReport: {description: "HTML report file."}
+ reportZip: {description: "Source data file."}
+ summary: {description: "Summary file."}
+ rawReport: {description: "Raw report file."}
+ images: {description: "Images in report file."}
}
meta {
WDL_AID: {
- exclude: ["NoneFile", "NoneArray"]
+ exclude: ["noneFile", "noneArray"]
}
}
}
task GetConfiguration {
input {
+ String memory = "2G" # Needs more than 1 to pull the docker image.
Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/fastqc:0.11.7--4"
}
@@ -155,14 +166,20 @@ task GetConfiguration {
}
runtime {
- memory: "2G" # Needs more than 1 to pull the docker image
+ memory: memory
time_minute: timeMinutes
docker: dockerImage
}
parameter_meta {
+ # inputs
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ adapterList: {description: "List of adapters found."}
+ contaminantList: {description: "List of contaminants found."}
+ limits: {description: "Limits file."}
}
}
diff --git a/fastqsplitter.wdl b/fastqsplitter.wdl
index c523cf8a..4a02697c 100644
--- a/fastqsplitter.wdl
+++ b/fastqsplitter.wdl
@@ -1,7 +1,5 @@
version 1.0
-# MIT License
-#
# Copyright (c) 2019 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -26,19 +24,24 @@ task Fastqsplitter {
input {
File inputFastq
Array[String]+ outputPaths
- String dockerImage = "quay.io/biocontainers/fastqsplitter:1.1.0--py37h516909a_1"
+
Int? compressionLevel
Int? threadsPerFile
- # fastqplitter utilizes one thread per input file and one or more threads per output file + one thread for the application.
- # Since a compression level of 1 is used, each output file uses approx 0.5 cores.
+
+ # fastqplitter utilizes one thread per input file and one or
+ # more threads per output file + one thread for the application.
+ # Since a compression level of 1 is used, each output file
+ # uses approx 0.5 cores.
Int cores = 1 + ceil(0.5 * length(outputPaths))
+ String dockerImage = "quay.io/biocontainers/fastqsplitter:1.1.0--py37h516909a_1"
}
# Busybox mkdir does not accept multiple paths.
command <<<
set -e
for FILE in ~{sep=' ' outputPaths}
- do mkdir -p "$(dirname $FILE)"
+ do
+ mkdir -p "$(dirname ${FILE})"
done
fastqsplitter \
~{"-c " + compressionLevel} \
@@ -51,15 +54,16 @@ task Fastqsplitter {
Array[File] chunks = outputPaths
}
- # Using very safe margins here. 10MB/300MB per outputfile is used for single-threaded/multi-threaded compression.
+ # Using very safe margins here. 10MB/300MB per outputfile is used for
+ # single-threaded/multi-threaded compression.
Float memoryPerFile = if select_first([threadsPerFile, 1]) > 1 then 0.40 else 0.02
Int fastqsplitterMemory = ceil(0.100 + memoryPerFile * length(outputPaths))
- # Make sure a minimum of 2 GB is present to pull the singularity image
+ # Make sure a minimum of 2 GB is present to pull the singularity image.
Int memory = if fastqsplitterMemory <= 2 then 2 else fastqsplitterMemory
runtime {
- memory: "~{memory}G"
- docker: dockerImage
cpu: cores
+ memory: "~{memory}GiB"
+ docker: dockerImage
}
}
diff --git a/fgbio.wdl b/fgbio.wdl
new file mode 100644
index 00000000..15fb0ea4
--- /dev/null
+++ b/fgbio.wdl
@@ -0,0 +1,68 @@
+version 1.0
+
+# Copyright (c) 2017 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task AnnotateBamWithUmis {
+ input {
+ File inputBam
+ File inputUmi
+ String outputPath
+
+ String memory = "120GiB"
+ Int timeMinutes = 360
+ String javaXmx="100G"
+ String dockerImage = "quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ fgbio -Xmx~{javaXmx} \
+ AnnotateBamWithUmis \
+ -i ~{inputBam} \
+ -f ~{inputUmi} \
+ -o ~{outputPath}
+ }
+
+ output {
+ File outputBam = outputPath
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputBam: {description: "The input BAM file.", category: "required"}
+ inputUmi: {description: "The input fastq file with UMIs.", category: "required"}
+ outputPath: {description: "Output directory path + output file.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: "UMI-annotated output BAM file."}
+ }
+}
diff --git a/flash.wdl b/flash.wdl
index 6e704921..7b50e0d7 100644
--- a/flash.wdl
+++ b/flash.wdl
@@ -24,16 +24,17 @@ import "common.wdl" as common
task Flash {
input {
- String? preCommand
FastqPair inputFastq
String outdirPath
String outPrefix = "flash"
+ Boolean compress = true
+
+ String? preCommand
Int? minOverlap
Int? maxOverlap
- Boolean compress = true
Int threads = 2
- String memory = "2G"
+ String memory = "2GiB"
}
command {
@@ -55,8 +56,8 @@ task Flash {
File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
FastqPair notCombined = object {
- R1: notCombined1,
- R2: notCombined2
+ R1: notCombined1,
+ R2: notCombined2
}
File hist = outdirPath + "/" + outPrefix + ".hist"
File histogram = outdirPath + "/" + outPrefix + ".histogram"
@@ -66,5 +67,4 @@ task Flash {
cpu: threads
memory: memory
}
-
-}
\ No newline at end of file
+}
diff --git a/gatk.wdl b/gatk.wdl
index e0209a0c..655a0b66 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -28,12 +28,13 @@ task AnnotateIntervals {
String annotatedIntervalsPath = "intervals.annotated.tsv"
File intervals
String intervalMergingRule = "OVERLAPPING_ONLY"
+ Int featureQueryLookahead = 1000000
+
File? mappabilityTrack
File? segmentalDuplicationTrack
- Int featureQueryLookahead = 1000000
- String memory = "3G"
String javaXmx = "2G"
+ String memory = "3GiB"
Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -57,12 +58,13 @@ task AnnotateIntervals {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
@@ -71,17 +73,18 @@ task AnnotateIntervals {
intervalMergingRule: {description: "Equivalent to gatk AnnotateIntervals' `--interval-merging-rule` option.", category: "advanced"}
mappabilityTrack: {description: "Equivalent to gatk AnnotateIntervals' `--mappability-track` option.", category: "common"}
segmentalDuplicationTrack: {description: "Equivalent to gatk AnnotateIntervals' `--segmenta-duplicarion-track` option.", category: "common"}
- featureQueryLookahead: {description: "Equivalent to gatk AnnotateIntervals' `--feature-query-lookahead` option", category: "advanced"}
+ featureQueryLookahead: {description: "Equivalent to gatk AnnotateIntervals' `--feature-query-lookahead` option.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ annotatedIntervals: {description: "This is a tab-separated values (TSV) file with a SAM-style header containing a sequence dictionary, a row specifying the column headers for the contained annotations, and the corresponding entry rows."}
}
}
-# Apply Base Quality Score Recalibration (BQSR) model
+# Apply Base Quality Score Recalibration (BQSR) model.
task ApplyBQSR {
input {
File inputBam
@@ -93,9 +96,11 @@ task ApplyBQSR {
File referenceFastaDict
File referenceFastaFai
- Int memoryMb = javaXmxMb + 512
Int javaXmxMb = 2048
- Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
+ Int memoryMb = javaXmxMb + 512
+ # This will likely be used with intervals, as such size based
+ # estimation can't be used.
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -124,33 +129,34 @@ task ApplyBQSR {
}
runtime {
- docker: dockerImage
+ memory: "~{memoryMb}MiB"
time_minutes: timeMinutes
- memory: "~{memoryMb}M"
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBam: {description: "The BAM file which should be recalibrated.", category: "required"}
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
outputBamPath: {description: "The location the resulting BAM file should be written.", category: "required"}
recalibrationReport: {description: "The BQSR report the be used for recalibration.", category: "required"}
sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
-
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ recalibratedBam: {description: "A BAM file containing the recalibrated read data."}
+ recalibratedBamIndex: {description: "Index of recalibrated BAM file."}
+ recalibratedBamMd5: {description: "MD5 of recalibrated BAM file."}
}
}
-# Generate Base Quality Score Recalibration (BQSR) model
+# Generate Base Quality Score Recalibration (BQSR) model.
task BaseRecalibrator {
input {
File inputBam
@@ -159,14 +165,15 @@ task BaseRecalibrator {
Array[File] sequenceGroupInterval = []
Array[File] knownIndelsSitesVCFs = []
Array[File] knownIndelsSitesVCFIndexes = []
- File? dbsnpVCF
- File? dbsnpVCFIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- Int memoryMb = javaXmxMb + 512
+ File? dbsnpVCF
+ File? dbsnpVCFIndex
+
Int javaXmxMb = 1024
+ Int memoryMb = javaXmxMb + 512
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -190,42 +197,42 @@ task BaseRecalibrator {
}
runtime {
- docker: dockerImage
+ memory: "~{memoryMb}MiB"
time_minutes: timeMinutes
- memory: "~{memoryMb}M"
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBam: {description: "The BAM file to generate a BQSR report for.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
recalibrationReportPath: {description: "The location to write the BQSR report to.", category: "required"}
sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
knownIndelsSitesVCFs: {description: "VCF files with known indels.", category: "advanced"}
knownIndelsSitesVCFIndexes: {description: "The indexed for the known variant VCFs.", category: "advanced"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
- referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
-
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ recalibrationReport: {description: "A GATK Report file with many tables."}
}
}
task CalculateContamination {
input {
File tumorPileups
+
File? normalPileups
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13GiB"
Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -246,20 +253,23 @@ task CalculateContamination {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
tumorPileups: {description: "The pileup summary of a tumor/case sample.", category: "required"}
normalPileups: {description: "The pileup summary of the normal/control sample.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ contaminationTable: {description: "Table with fractions of reads from cross-sample contamination."}
+ mafTumorSegments: {description: "Tumor segments table."}
}
}
@@ -268,8 +278,8 @@ task CallCopyRatioSegments {
String outputPrefix
File copyRatioSegments
- String memory = "3G"
String javaXmx = "2G"
+ String memory = "3GiB"
Int timeMinutes = 2
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -289,20 +299,23 @@ task CallCopyRatioSegments {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
outputPrefix: {description: "The prefix for the output files.", category: "required"}
copyRatioSegments: {description: "The copy ratios file generated by gatk ModelSegments.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ calledSegments: {description: "This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in CalledCopyRatioSegmentCollection.CalledCopyRatioSegmentTableColumn, and the corresponding entry rows."}
+ calledSegmentsIgv: {description: "This is a tab-separated values (TSV) file with CBS-format column headers and the corresponding entry rows that can be plotted using IGV."}
}
}
@@ -310,15 +323,16 @@ task CollectAllelicCounts {
input {
String allelicCountsPath = "allelic_counts.tsv"
File commonVariantSites
- File? commonVariantSitesIndex
File inputBam
File inputBamIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- String memory = "11G"
+ File? commonVariantSitesIndex
+
String javaXmx = "10G"
+ String memory = "11GiB"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -339,26 +353,28 @@ task CollectAllelicCounts {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
allelicCountsPath: {description: "The path the output should be written to.", category: "advanced"}
commonVariantSites: {description: "Interval list or vcf of common variant sites (to retrieve the allelic counts for).", category: "required"}
- commonVariantSitesIndex: {description: "The index for commonVariantSites.", category: "common"}
inputBam: {description: "The BAM file to generate counts for.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ commonVariantSitesIndex: {description: "The index for commonVariantSites.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ allelicCounts: {description: "This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in AllelicCountCollection.AllelicCountTableColumn, and the corresponding entry rows."}
}
}
@@ -373,8 +389,8 @@ task CollectReadCounts {
File referenceFastaFai
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "8G"
String javaXmx = "7G"
+ String memory = "8GiB"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 5)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -397,12 +413,13 @@ task CollectReadCounts {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
countsPath: {description: "The location the output should be written to.", category: "advanced"}
intervals: {description: "The intervals to collect counts for.", category: "required"}
inputBam: {description: "The BAM file to determine the coverage for.", category: "required"}
@@ -411,12 +428,13 @@ task CollectReadCounts {
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
intervalMergingRule: {description: "Equivalent to gatk CollectReadCounts' `--interval-merging-rule` option.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ counts: {description: "Read counts at specified intervals."}
}
}
@@ -430,8 +448,8 @@ task CombineGVCFs {
File referenceFastaDict
File referenceFastaFai
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5GiB"
Int timeMinutes = 1 + ceil(size(gvcfFiles, "G") * 8)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -453,28 +471,28 @@ task CombineGVCFs {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
gvcfFiles: {description: "The GVCF files to be combined.", category: "required"}
gvcfFilesIndex: {description: "The indexes for the GVCF files.", caregory: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
outputPath: {description: "The location the combined GVCF should be written to.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "A combined multi-sample gVCF."}
+ outputVcfIndex: {description: "Index of the output file."}
}
}
@@ -486,12 +504,12 @@ task CombineVariants {
String genotypeMergeOption = "UNIQUIFY"
String filteredRecordsMergeType = "KEEP_IF_ANY_UNFILTERED"
Array[String]+ identifiers
- Array[File]+ variantVcfs # follow "identifiers" array order
+ Array[File]+ variantVcfs # Follow "identifiers" array order.
Array[File]+ variantIndexes
String outputPath
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13GiB"
Int timeMinutes = 180
String dockerImage = "broadinstitute/gatk3:3.8-1"
}
@@ -499,17 +517,17 @@ task CombineVariants {
command <<<
set -e
mkdir -p "$(dirname ~{outputPath})"
-
- # build "-V: " arguments according to IDs and VCFs to merge
- # Make sure commands are run in bash
+ # Build "-V: " arguments according to IDs
+ # and VCFs to merge.
+ # Make sure commands are run in bash.
V_args=$(bash -c '
set -eu
ids=(~{sep=" " identifiers})
vars=(~{sep=" " variantVcfs})
for (( i = 0; i < ${#ids[@]}; ++i ))
- do
+ do
printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
- done
+ done
')
java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 -jar /usr/GenomeAnalysisTK.jar \
-T CombineVariants \
@@ -526,12 +544,13 @@ task CombineVariants {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
@@ -540,14 +559,15 @@ task CombineVariants {
identifiers: {description: "The sample identifiers in the same order as variantVcfs.", category: "required"}
variantVcfs: {description: "The input VCF files in the same order as identifiers.", category: "required"}
variantIndexes: {description: "The indexes of the input VCF files.", category: "required"}
- outputPath: {description: "The location the output should be written to", category: "required"}
-
+ outputPath: {description: "The location the output should be written to.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ combinedVcf: {description: "Combined VCF file."}
+ combinedVcfIndex: {description: "Index of combined VCF file."}
}
}
@@ -555,12 +575,14 @@ task CreateReadCountPanelOfNormals {
input {
String PONpath = "PON.hdf5"
Array[File]+ readCountsFiles
+
File? annotatedIntervals
- String memory = "8G"
String javaXmx = "7G"
+ String memory = "8GiB"
Int timeMinutes = 5
- String dockerImage = "broadinstitute/gatk:4.1.8.0" # The biocontainer causes a spark related error for some reason...
+ # The biocontainer causes a spark related error for some reason.
+ String dockerImage = "broadinstitute/gatk:4.1.8.0"
}
command {
@@ -578,34 +600,36 @@ task CreateReadCountPanelOfNormals {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
PONpath: {description: "The location the PON should be written to.", category: "common"}
readCountsFiles: {description: "The read counts files as generated by CollectReadCounts.", category: "required"}
- annotatedIntervals: {description: "An annotation set of intervals as generated by AnnotateIntervals. If provided, explicit GC correction will be performed.",
- category: "advanced"}
+ annotatedIntervals: {description: "An annotation set of intervals as generated by AnnotateIntervals. If provided, explicit GC correction will be performed.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ PON: {description: "Panel-of-normals file."}
}
}
task DenoiseReadCounts {
input {
- File? PON
- File? annotatedIntervals
File readCounts
String outputPrefix
- String memory = "5G"
+ File? PON
+ File? annotatedIntervals
+
String javaXmx = "4G"
+ String memory = "5GiB"
Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -628,23 +652,25 @@ task DenoiseReadCounts {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- PON: {description: "A panel of normals as generated by CreateReadCountPanelOfNormals.", category: "advanced"}
- annotatedIntervals: {description: "An annotated set of intervals as generated by AnnotateIntervals. Will be ignored if PON is provided.",
- category: "advanced"}
+ # inputs
readCounts: {description: "The read counts file as generated by CollectReadCounts.", category: "required"}
outputPrefix: {description: "The prefix for the output files.", category: "required"}
+ PON: {description: "A panel of normals as generated by CreateReadCountPanelOfNormals.", category: "advanced"}
+ annotatedIntervals: {description: "An annotated set of intervals as generated by AnnotateIntervals. Will be ignored if PON is provided.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ standardizedCopyRatios: {description: "This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in CopyRatioCollection.CopyRatioTableColumn, and the corresponding entry rows."}
+ denoisedCopyRatios: {description: "This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in CopyRatioCollection.CopyRatioTableColumn, and the corresponding entry rows."}
}
}
@@ -656,14 +682,15 @@ task FilterMutectCalls {
File unfilteredVcf
File unfilteredVcfIndex
String outputVcf
+ Int uniqueAltReadCount = 4
+ File mutect2Stats
+
File? contaminationTable
File? mafTumorSegments
File? artifactPriors
- Int uniqueAltReadCount = 4
- File mutect2Stats
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13GiB"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -692,41 +719,44 @@ task FilterMutectCalls {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
unfilteredVcf: {description: "An unfiltered VCF file as produced by Mutect2.", category: "required"}
unfilteredVcfIndex: {description: "The index of the unfiltered VCF file.", category: "required"}
outputVcf: {description: "The location the filtered VCF file should be written.", category: "required"}
+ uniqueAltReadCount: {description: "Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.", category: "advanced"}
+ mutect2Stats: {description: "Equivalent to FilterMutectCalls' `-stats` option.", category: "advanced"}
contaminationTable: {description: "Equivalent to FilterMutectCalls' `--contamination-table` option.", category: "advanced"}
mafTumorSegments: {description: "Equivalent to FilterMutectCalls' `--tumor-segmentation` option.", category: "advanced"}
artifactPriors: {description: "Equivalent to FilterMutectCalls' `--ob-priors` option.", category: "advanced"}
- uniqueAltReadCount: {description: "Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.", category: "advanced"}
- mutect2Stats: {description: "Equivalent to FilterMutectCalls' `-stats` option.", category: "advanced"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ filteredVcf: {description: "VCF file with filtered variants from a Mutect2 VCF callset."}
+ filteredVcfIndex: {description: "Index of output VCF file."}
+ filteringStats: {description: "The output filtering stats file."}
}
}
-# Combine multiple recalibration tables from scattered BaseRecalibrator runs
+# Combine multiple recalibration tables from scattered BaseRecalibrator runs.
task GatherBqsrReports {
input {
Array[File] inputBQSRreports
String outputReportPath
- Int memoryMb = 256 + javaXmxMb
Int javaXmxMb = 256
+ Int memoryMb = 256 + javaXmxMb
Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -745,21 +775,22 @@ task GatherBqsrReports {
}
runtime {
- docker: dockerImage
+ memory: "~{memoryMb}MiB"
time_minutes: timeMinutes
- memory: "~{memoryMb}M"
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBQSRreports: {description: "The BQSR reports to be merged.", category: "required"}
outputReportPath: {description: "The location of the combined BQSR report.", category: "required"}
-
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBQSRreport: {description: "Single file with scattered BQSR recalibration reports gathered into one."}
}
}
@@ -770,9 +801,11 @@ task GenomicsDBImport {
Array[File]+ intervals
String genomicsDBWorkspacePath = "genomics_db"
String genomicsDBTarFile = "genomics_db.tar.gz"
+
String? tmpDir
- String memory = "5G"
+
String javaXmx = "4G"
+ String memory = "5GiB"
Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -794,25 +827,26 @@ task GenomicsDBImport {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
gvcfFiles: {description: "The gvcfFiles to be merged.", category: "required"}
gvcfFilesIndex: {description: "Indexes for the gvcfFiles.", category: "required"}
intervals: {description: "intervals over which to operate.", category: "required"}
- genomicsDBWorkspacePath: {description: "Where the genomicsDB files should be stored", category: "advanced"}
- genomicsDBTarFile: {description: "Where the .tar file containing the genomicsDB should be stored", category: "advanced"}
- tmpDir: {description: "Alternate temporary directory in case there is not enough space. Must be mounted when using containers",
- category: "advanced"}
+ genomicsDBWorkspacePath: {description: "Where the genomicsDB files should be stored.", category: "advanced"}
+ genomicsDBTarFile: {description: "Where the .tar file containing the genomicsDB should be stored.", category: "advanced"}
+ tmpDir: {description: "Alternate temporary directory in case there is not enough space. Must be mounted when using containers.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ genomicsDbTarArchive: {description: "Imported VCFs to GenomicsDB file."}
}
}
@@ -820,18 +854,19 @@ task GenotypeGVCFs {
input {
File gvcfFile
File gvcfFileIndex
- Array[File]+ intervals
String outputPath
File referenceFasta
File referenceFastaDict
File referenceFastaFai
Array[String] annotationGroups = ["StandardAnnotation"]
+
+ Array[File]? intervals
File? dbsnpVCF
File? dbsnpVCFIndex
File? pedigree
- String memory = "7G"
String javaXmx = "6G"
+ String memory = "7GiB"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -846,43 +881,43 @@ task GenotypeGVCFs {
~{"-D " + dbsnpVCF} \
~{"--pedigree " + pedigree} \
~{true="-G" false="" length(annotationGroups) > 0} ~{sep=" -G " annotationGroups} \
- --only-output-calls-starting-in-intervals \
-V ~{gvcfFile} \
- -L ~{sep=' -L ' intervals}
+ ~{true="--only-output-calls-starting-in-intervals" false="" defined(intervals)} \
+ ~{true="-L" false="" defined(intervals)} ~{sep=' -L ' intervals}
}
output {
File outputVCF = outputPath
File outputVCFIndex = outputPath + ".tbi"
-
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
gvcfFile: {description: "The GVCF file to be genotyped.", category: "required"}
gvcfFileIndex: {description: "The index of the input GVCF file.", category: "required"}
- intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"}
outputPath: {description: "The location to write the output VCF file to.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- annotationGroups: {description: "Which annotation groups will be used for the annotation", category: "advanced"}
+ annotationGroups: {description: "Which annotation groups will be used for the annotation.", category: "advanced"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "optional"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- pedigree: {description: "Pedigree file for determining the population \"founders\"", category: "common"}
+ pedigree: {description: "Pedigree file for determining the population \"founders\".", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVCF: {description: "A final VCF in which all samples have been jointly genotyped. "}
+ outputVCFIndex: {description: "Index of final VCF file."}
}
}
@@ -896,8 +931,8 @@ task GetPileupSummaries {
File sitesForContaminationIndex
String outputPrefix
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13GiB"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -917,12 +952,13 @@ task GetPileupSummaries {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
sampleBam: {description: "A BAM file for which a pileup should be created.", category: "required"}
sampleBamIndex: {description: "The index of the input BAM file.", category: "required"}
variantsForContamination: {description: "A VCF file with common variants.", category: "required"}
@@ -930,13 +966,13 @@ task GetPileupSummaries {
sitesForContamination: {description: "A bed file describing regions to operate on.", category: "required"}
sitesForContaminationIndex: {description: "The index for the bed file.", category: "required"}
outputPrefix: {description: "The prefix for the ouput.", category: "required"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ pileups: {description: "Pileup metrics for inferring contamination."}
}
}
@@ -945,26 +981,27 @@ task HaplotypeCaller {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
- Array[File]+? intervalList
- Array[File]+? excludeIntervalList
String outputPath
File referenceFasta
File referenceFastaIndex
File referenceFastaDict
+ Boolean gvcf = false
+ String emitRefConfidence = if gvcf then "GVCF" else "NONE"
+ Boolean dontUseSoftClippedBases = false
+
+ Array[File]+? intervalList
+ Array[File]+? excludeIntervalList
Float? contamination
File? dbsnpVCF
File? dbsnpVCFIndex
File? pedigree
Int? ploidy
String? outputMode
- Boolean gvcf = false
- String emitRefConfidence = if gvcf then "GVCF" else "NONE"
- Boolean dontUseSoftClippedBases = false
Float? standardMinConfidenceThresholdForCalling
- Int memoryMb = javaXmxMb + 512
- # Memory increases with time used. 4G should cover most use cases.
Int javaXmxMb = 4096
+ # Memory increases with time used. 4G should cover most use cases.
+ Int memoryMb = javaXmxMb + 512
Int timeMinutes = 400 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -995,50 +1032,48 @@ task HaplotypeCaller {
}
runtime {
- docker: dockerImage
+ memory: "~{memoryMb}MiB"
time_minutes: timeMinutes
- memory: "~{memoryMb}M"
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
- intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
- excludeIntervalList: {description: "Bed files or interval lists describing the regions to NOT operate on.", category: "common"}
outputPath: {description: "The location to write the output to.", category: "required"}
- ploidy: {description: "The ploidy with which the variants should be called.", category: "common"}
- gvcf: {description: "Whether the output should be a gvcf", category: "common"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaIndex: {description: "The index for the reference fasta file.", category: "required"}
- contamination: {description: "Equivalent to HaplotypeCaller's `-contamination` option.", category: "advanced"}
- outputMode: {description: "Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.",
- category: "advanced"}
- emitRefConfidence: {description: "Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'",
- category: "advanced"}
+ gvcf: {description: "Whether the output should be a gvcf.", category: "common"}
+ emitRefConfidence: {description: "Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'.", category: "advanced"}
dontUseSoftClippedBases: {description: "Do not use soft-clipped bases. Should be 'true' for RNA variant calling.", category: "common"}
- standardMinConfidenceThresholdForCalling: {description: "Confidence threshold used for calling variants.", category: "advanced"}
+ intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
+ excludeIntervalList: {description: "Bed files or interval lists describing the regions to NOT operate on.", category: "common"}
+ contamination: {description: "Equivalent to HaplotypeCaller's `-contamination` option.", category: "advanced"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- pedigree: {description: "Pedigree file for determining the population \"founders\"", category: "common"}
+ pedigree: {description: "Pedigree file for determining the population \"founders\".", category: "common"}
+ ploidy: {description: "The ploidy with which the variants should be called.", category: "common"}
+ outputMode: {description: "Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.", category: "advanced"}
+ standardMinConfidenceThresholdForCalling: {description: "Confidence threshold used for calling variants.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVCF: {description: "Raw, unfiltered SNP and indel calls."}
+ outputVCFIndex: {description: "Index of output VCF."}
}
}
-
task LearnReadOrientationModel {
input {
Array[File]+ f1r2TarGz
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13GiB"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1056,19 +1091,21 @@ task LearnReadOrientationModel {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
f1r2TarGz: {description: "A f1r2TarGz file outputed by mutect2.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ artifactPriorsTable: {description: "Maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter."}
}
}
@@ -1076,8 +1113,8 @@ task MergeStats {
input {
Array[File]+ stats
- String memory = "15G"
String javaXmx = "14G"
+ String memory = "15GiB"
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1095,19 +1132,21 @@ task MergeStats {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
stats: {description: "Statistics files to be merged.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ mergedStats: {description: "Merged stats from scattered Mutect2 runs."}
}
}
@@ -1117,14 +1156,13 @@ task ModelSegments {
String outputPrefix
File denoisedCopyRatios
File allelicCounts
- File? normalAllelicCounts
- Int minimumTotalAlleleCountCase = if defined(normalAllelicCounts)
- then 0
- else 30
+ Int minimumTotalAlleleCountCase = if defined(normalAllelicCounts) then 0 else 30
Int maximumNumberOfSmoothingIterations = 10
- String memory = "11G"
+ File? normalAllelicCounts
+
String javaXmx = "10G"
+ String memory = "11GiB"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1145,7 +1183,6 @@ task ModelSegments {
output {
File hetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.tsv"
- File? normalHetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.normal.tsv"
File copyRatioSegments = outputDir + "/" + outputPrefix + ".cr.seg"
File copyRatioCBS = outputDir + "/" + outputPrefix + ".cr.igv.seg"
File alleleFractionCBS = outputDir + "/" + outputPrefix + ".af.igv.seg"
@@ -1155,29 +1192,41 @@ task ModelSegments {
File modeledSegments = outputDir + "/" + outputPrefix + ".modelFinal.seg"
File copyRatioParameters = outputDir + "/" + outputPrefix + ".modelFinal.cr.param"
File alleleFractionParameters = outputDir + "/" + outputPrefix + ".modelFinal.af.param"
+ File? normalHetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.normal.tsv"
}
runtime {
- docker: dockerImage
- time_minute: timeMinutes
memory: memory
+ time_minute: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
outputDir: {description: "The directory to write the ouput to.", category: "common"}
outputPrefix: {description: "The prefix of the output files. Should not include directories.", category: "required"}
denoisedCopyRatios: {description: "The denoised copy ratios as generated by DenoiseReadCounts.", category: "required"}
allelicCounts: {description: "The allelicCounts as generate by CollectAllelicCounts.", category: "required" }
- normalAllelicCounts: {description: "The allelicCounts as generate by CollectAllelicCounts for a matched normal.", category: "common"}
minimumTotalAlleleCountCase: {description: "Equivalent to gatk ModelSeqments' `--minimum-total-allele-count-case` option.", category: "advanced"}
maximumNumberOfSmoothingIterations: {description: "Equivalent to gatk ModelSeqments' `--maximum-number-of-smoothing-iterations` option.", category: "advanced"}
-
+ normalAllelicCounts: {description: "The allelicCounts as generate by CollectAllelicCounts for a matched normal.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ hetrozygousAllelicCounts: {description: "Allelic-counts file containing the counts at sites genotyped as heterozygous in the case sample."}
+ copyRatioSegments: {description: "It contains the segments from the .modelFinal.seg file converted to a format suitable for input to CallCopyRatioSegments."}
+ copyRatioCBS: {description: "The posterior medians of the log2 copy ratio."}
+ alleleFractionCBS: {description: "Minor-allele fraction."}
+ unsmoothedModeledSegments: {description: "The initial modeled-segments result before segmentation smoothing."}
+ unsmoothedCopyRatioParameters: {description: "The initial copy-ratio-model global-parameter result before segmentation smoothing."}
+ unsmoothedAlleleFractionParameters: {description: "The initial allele-fraction-model global-parameter result before segmentation smoothing."}
+ modeledSegments: {description: "The final modeled-segments result after segmentation smoothing."}
+ copyRatioParameters: {description: "The final copy-ratio-model global-parameter result after segmentation smoothing."}
+ alleleFractionParameters: {description: "The final allele-fraction-model global-parameter result after segmentation smoothing."}
+ normalHetrozygousAllelicCounts: {description: "Allelic-counts file containing the counts at sites genotyped as heterozygous in the matched-normal sample."}
}
}
@@ -1190,17 +1239,18 @@ task MuTect2 {
File referenceFastaFai
String outputVcf
String tumorSample
+ String f1r2TarGz = "f1r2.tar.gz"
+ Array[File]+ intervals
+ String outputStats = outputVcf + ".stats"
+
String? normalSample
File? germlineResource
File? germlineResourceIndex
File? panelOfNormals
File? panelOfNormalsIndex
- String f1r2TarGz = "f1r2.tar.gz"
- Array[File]+ intervals
- String outputStats = outputVcf + ".stats"
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5GiB"
Int timeMinutes = 240
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1229,12 +1279,13 @@ task MuTect2 {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
@@ -1242,20 +1293,24 @@ task MuTect2 {
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
tumorSample: {description: "The name of the tumor/case sample.", category: "required"}
+ f1r2TarGz: {description: "Equivalent to Mutect2's `--f1r2-tar-gz` option.", category: "advanced"}
+ intervals: {description: "Bed files describing the regiosn to operate on.", category: "required"}
+ outputStats: {description: "The location the output statistics should be written to.", category: "advanced"}
normalSample: {description: "The name of the normal/control sample.", category: "common"}
germlineResource: {description: "Equivalent to Mutect2's `--germline-resource` option.", category: "advanced"}
germlineResourceIndex: {description: "The index for the germline resource.", category: "advanced"}
panelOfNormals: {description: "Equivalent to Mutect2's `--panel-of-normals` option.", category: "advanced"}
panelOfNormalsIndex: {description: "The index for the panel of normals.", category: "advanced"}
- f1r2TarGz: {description: "Equivalent to Mutect2's `--f1r2-tar-gz` option.", category: "advanced"}
- intervals: {description: "Bed files describing the regiosn to operate on.", category: "required"}
- outputStats: {description: "The location the output statistics should be written to.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ vcfFile: {description: "Somatic SNVs and indels called via local assembly of haplotypes."}
+ vcfFileIndex: {description: "Index for Mutect2 VCF."}
+ f1r2File: {description: "Contains information that can then be passed to LearnReadOrientationModel, which generate an artifact prior table for each tumor sample for FilterMutectCalls to use."}
+ stats: {description: "Stats file."}
}
}
@@ -1266,10 +1321,11 @@ task PlotDenoisedCopyRatios {
String outputPrefix
File standardizedCopyRatios
File denoisedCopyRatios
+
Int? minimumContigLength
- String memory = "4G"
String javaXmx = "3G"
+ String memory = "4GiB"
Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.8.0"
}
@@ -1289,32 +1345,39 @@ task PlotDenoisedCopyRatios {
output {
File denoisedCopyRatiosPlot = outputDir + "/" + outputPrefix + ".denoised.png"
- File? denoisedCopyRatiosLimitedPlot = outputDir + "/" + outputPrefix + ".denoisedLimit4.png"
File standardizedMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".standardizedMAD.txt"
File denoisedMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".denoisedMAD.txt"
File deltaMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".deltaMAD.txt"
File deltaScaledMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".scaledDeltaMAD.txt"
+ File? denoisedCopyRatiosLimitedPlot = outputDir + "/" + outputPrefix + ".denoisedLimit4.png"
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file used for the analyses.", category: "required"}
outputDir: {description: "The directory to write the ouput to.", category: "common"}
outputPrefix: {description: "The prefix of the output files. Should not include directories.", category: "required"}
- denoisedCopyRatios: {description: "The denoised copy ratios as generated by DenoiseReadCounts.", category: "required"}
standardizedCopyRatios: {description: "The standardized copy ratios as generated by DenoiseReadCounts.", category: "required"}
+ denoisedCopyRatios: {description: "The denoised copy ratios as generated by DenoiseReadCounts.", category: "required"}
minimumContigLength: {description: "The minimum length for a contig to be included in the plots.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ denoisedCopyRatiosPlot: {description: "Plot showing the entire range of standardized and denoised copy ratios."}
+ standardizedMedianAbsoluteDeviation: {description: "Standardized median absolute deviation copy ratios."}
+ denoisedMedianAbsoluteDeviation: {description: "Denoised median absolute deviation copy ratios."}
+ deltaMedianAbsoluteDeviation: {description: "The change between `standardizedMedianAbsoluteDeviation` & `denoisedMedianAbsoluteDeviation`."}
+ deltaScaledMedianAbsoluteDeviation: {description: "The change between `standardizedMedianAbsoluteDeviation` & `denoisedMedianAbsoluteDeviation` scaled by standardized MAD."}
+ denoisedCopyRatiosLimitedPlot: {description: "Plot showing the standardized and denoised copy ratios limited to ratios within [0, 4]."}
}
}
@@ -1326,10 +1389,11 @@ task PlotModeledSegments {
File denoisedCopyRatios
File segments
File allelicCounts
+
Int? minimumContigLength
- String memory = "4G"
String javaXmx = "3G"
+ String memory = "4GiB"
Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.8.0"
}
@@ -1353,12 +1417,13 @@ task PlotModeledSegments {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file used for the analyses.", category: "required"}
outputDir: {description: "The directory to write the ouput to.", category: "common"}
outputPrefix: {description: "The prefix of the output files. Should not include directories.", category: "required"}
@@ -1366,12 +1431,13 @@ task PlotModeledSegments {
segments: {description: "The modeled segments as generated by ModelSegments.", category: "required"}
allelicCounts: {description: "The hetrozygous allelic counts as generated by ModelSegments.", category: "required"}
minimumContigLength: {description: "The minimum length for a contig to be included in the plots.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ modeledSegmentsPlot: {description: "This plot shows the input denoised copy ratios and/or alternate-allele fractions as points, as well as box plots for the available posteriors in each segment."}
}
}
@@ -1380,14 +1446,15 @@ task PreprocessIntervals {
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- File? intervals
String outputIntervalList = "bins.interval_list"
Int binLength = if defined(intervals) then 0 else 1000
Int padding = if defined(intervals) then 250 else 0
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "4G"
+ File? intervals
+
String javaXmx = "3G"
+ String memory = "4GiB"
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 6)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1411,41 +1478,47 @@ task PreprocessIntervals {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- referenceFasta: {description: "The reference fasta file..", category: "required"}
+ # inputs
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- intervals: {description: "Bed files describing the regiosn to operate on.", category: "common"}
outputIntervalList: {description: "The location the output should be written to.", category: "advanced"}
binLength: {description: "The size of the bins to be created. Should be 0 for targeted/exome sequencing.", category: "advanced"}
padding: {description: "The padding to be added to the bins. Should be 0 if contiguos binning is used, eg with WGS.", category: "advanced"}
intervalMergingRule: {description: "Equivalent to gatk PreprocessIntervals' `--interval-merging-rule` option.", category: "advanced"}
+ intervals: {description: "Bed files describing the regiosn to operate on.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ intervalList: {description: "Preprocessed Picard interval-list file."}
}
}
task SelectVariants {
input {
+ File inputVcf
+ File inputVcfIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- File inputVcf
- File inputVcfIndex
String outputPath = "output.vcf.gz"
- String? selectTypeToInclude
Array[File] intervals = []
- String memory = "5G"
+
+ Boolean excludeFiltered = false
+ String? selectTypeToInclude
+ String? selectGenotype
+
String javaXmx = "4G"
+ String memory = "5GiB"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1458,6 +1531,8 @@ task SelectVariants {
-R ~{referenceFasta} \
-V ~{inputVcf} \
~{"--select-type-to-include " + selectTypeToInclude} \
+ ~{"-select-genotype \"" + selectGenotype}~{true="\"" false="" defined(selectGenotype)} \
+ ~{true="--exclude-filtered" false="" excludeFiltered} \
~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals} \
-O ~{outputPath}
}
@@ -1468,29 +1543,31 @@ task SelectVariants {
}
runtime {
- docker: dockerImage
- time_minute: timeMinutes
memory: memory
+ time_minute: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputVcf: {description: "The VCF input file.", category: "required"}
inputVcfIndex: {description: "The input VCF file's index.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- selectTypeToInclude: {description: "Select only a certain type of variants from the input file", category: "common"}
outputPath: {description: "The location the output VCF file should be written.", category: "advanced"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
-
+ selectTypeToInclude: {description: "Select only a certain type of variants from the input file.", category: "common"}
+ excludeFiltered: {description: "Remove all variants that do not have a PASS filter", category: "advanced"}
+ selectGenotype: {description: "The genotype to be selected", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "A new VCF file containing the selected subset of variants."}
+ outputVcfIndex: {description: "Index of the new output VCF file."}
}
}
@@ -1504,8 +1581,8 @@ task SplitNCigarReads {
String outputBam
Array[File] intervals = []
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5GiB"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1527,28 +1604,28 @@ task SplitNCigarReads {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBam: {description: "The BAM file for which spliced reads should be split.", category: "required"}
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
outputBam: {description: "The location the output BAM file should be written.", category: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ bam: {description: "BAM file with reads split at N CIGAR elements and CIGAR strings updated."}
+ bamIndex: {description: "Index of output BAM file."}
}
}
@@ -1558,11 +1635,6 @@ task VariantEval {
Array[File] evalVcfsIndex
Array[File] comparisonVcfs = []
Array[File] comparisonVcfsIndex = []
- File? referenceFasta
- File? referenceFastaDict
- File? referenceFastaFai
- File? dbsnpVCF
- File? dbsnpVCFIndex
Array[File] intervals = []
String outputPath = "eval.table"
Boolean doNotUseAllStandardModules = false
@@ -1572,8 +1644,14 @@ task VariantEval {
Array[String] samples = []
Boolean mergeEvals = false
- String memory = "5G"
+ File? referenceFasta
+ File? referenceFastaDict
+ File? referenceFastaFai
+ File? dbsnpVCF
+ File? dbsnpVCFIndex
+
String javaXmx = "4G"
+ String memory = "5GiB"
# TODO: Refine estimate. For now 4 minutes per GB of input.
Int timeMinutes = ceil(size(flatten([evalVcfs, comparisonVcfs, select_all([referenceFasta, dbsnpVCF])]), "G") * 20)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
@@ -1604,35 +1682,40 @@ task VariantEval {
runtime {
cpu: 1
- docker: dockerImage
memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
+
parameter_meta {
+ # inputs
evalVcfs: {description: "Variant sets to evaluate.", category: "required"}
evalVcfsIndex: {description: "Indexes for the variant sets.", category: "required"}
comparisonVcfs: {description: "Compare set vcfs.", category: "advanced"}
comparisonVcfsIndex: {description: "Indexes for the compare sets.", category: "advanced"}
- evalModules: {description: "One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless doNotUseAllStandardModules=true)", category: "common"}
- stratificationModules: {description: "One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless doNotUseAllStandardStratifications=true)", category: "common"}
- samples: {description: "Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context." , category: "advanced"} # Advanced because this description is impossible to understand...
- mergeEvals: {description: "If provided, all evalVcf tracks will be merged into a single eval track", category: "common"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
+ outputPath: {description: "The location the output table should be written.", category: "advanced"}
doNotUseAllStandardModules: {description: "Do not use the standard modules by default (instead, only those that are specified with the evalModules option).", category: "common"}
doNotUseAllStandardStratifications: {description: "Do not use the standard stratification modules by default (instead, only those that are specified with the stratificationModules option).", category: "common"}
+ evalModules: {description: "One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless doNotUseAllStandardModules=true).", category: "common"}
+ stratificationModules: {description: "One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless doNotUseAllStandardStratifications=true).", category: "common"}
+ samples: {description: "Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context." , category: "advanced"}
+ mergeEvals: {description: "If provided, all evalVcf tracks will be merged into a single eval track.", category: "common"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "common"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "common"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "common"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- outputPath: {description: "The location the output table should be written.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ table: {description: "Evaluation tables detailing the results of the eval modules which were applied."}
}
}
+
task VariantFiltration {
input {
File inputVcf
@@ -1644,8 +1727,8 @@ task VariantFiltration {
Array[String]+ filterArguments
Array[File] intervals = []
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5GiB"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1668,29 +1751,28 @@ task VariantFiltration {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputVcf: {description: "The VCF to be filtered.", category: "required"}
inputVcfIndex: {description: "The input VCF file's index.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ filterArguments: {description: "Arguments that should be used for the filter. For example: ['--filter-name', 'my_filter', '--filter-expression', 'AB<0.2'].", category: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
- filterArguments: {description: "Arguments that should be used for the filter. For example: ['--filter-name', 'my_filter', '--filter-expression', 'AB<0.2']",
- category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ filteredVcf: {description: "A filtered VCF in which passing variants are annotated as PASS and failing variants are annotated with the name(s) of the filter(s) they failed."}
+ filteredVcfIndex: {description: "Index of filtered VCF."}
}
}
-
diff --git a/gffcompare.wdl b/gffcompare.wdl
index e5f62b5e..fe1db0a8 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -22,16 +22,10 @@ version 1.0
task GffCompare {
input {
- File? inputGtfList
Array[File] inputGtfFiles
- File referenceAnnotation
- String? outputDir
- String outPrefix = "gffcmp" # gffcmp is the default used by the program as well. This
- # needs to be defined in order for the output values to be consistent and correct.
- File? genomeSequences
- Int? maxDistanceFreeEndsTerminalExons
- Int? maxDistanceGroupingTranscriptStartSites
- String? namePrefix
+ # gffcmp is the default used by the program as well. This needs to be
+ # defined in order for the output values to be consistent and correct.
+ String outPrefix = "gffcmp"
Boolean C = false
Boolean A = false
Boolean X = false
@@ -44,15 +38,24 @@ task GffCompare {
Boolean verbose = false
Boolean debugMode = false
- Int timeMinutes = 1 + ceil(size(inputGtfFiles, "G") * 30)
+ File? inputGtfList
+ File? referenceAnnotation
+ String? outputDir
+ File? genomeSequences
+ Int? maxDistanceFreeEndsTerminalExons
+ Int? maxDistanceGroupingTranscriptStartSites
+ String? namePrefix
+
+ String memory = "4GiB"
+ Int timeMinutes = 1 + ceil(size(inputGtfFiles, "GiB") * 30)
String dockerImage = "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
# This workaround only works in the input section.
- # Issue addressed at https://github.com/openwdl/wdl/pull/263
+ # Issue addressed at https://github.com/openwdl/wdl/pull/263.
File? noneFile # This is a wdl workaround. Please do not assign!
}
- # This allows for the creation of output directories
+ # This allows for the creation of output directories.
String dirPrefix = if defined(outputDir)
then select_first([outputDir]) + "/"
else ""
@@ -62,7 +65,7 @@ task GffCompare {
set -e
~{"mkdir -p " + outputDir}
gffcompare \
- -r ~{referenceAnnotation} \
+ ~{"-r " + referenceAnnotation} \
~{"-o '" + totalPrefix + "'"} \
~{"-s " + genomeSequences} \
~{"-e " + maxDistanceFreeEndsTerminalExons} \
@@ -89,43 +92,39 @@ task GffCompare {
else 0
Int noInputFiles = length(inputGtfFiles)
Boolean oneFile = (noFilesGtfList + noInputFiles) == 1
- String annotatedName = if oneFile
+ String annotatedName = if oneFile && defined(referenceAnnotation)
then "annotated"
else "combined"
- # Check if a redundant .gtf will be created
+ # Check if a redundant .gtf will be created.
Boolean createRedundant = C || A || X
output {
+ # noneFile is not stable. Please replace this as soon as wdl spec allows.
File annotated = totalPrefix + "." + annotatedName + ".gtf"
File loci = totalPrefix + ".loci"
File stats = totalPrefix + ".stats"
File tracking = totalPrefix + ".tracking"
- # noneFile is not stable. Please replace this as soon as wdl spec allows
+ Array[File] allFiles = select_all([annotated, loci, stats, tracking, redundant, missedIntrons])
File? redundant = if createRedundant
then totalPrefix + ".redundant.gtf"
else noneFile
File? missedIntrons = if debugMode
then totalPrefix + ".missed_introns.gtf"
else noneFile
- Array[File] allFiles = select_all([annotated, loci, stats, tracking, redundant, missedIntrons])
}
runtime {
- time_minutes: timeMinutes
- docker: dockerImage
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- inputGtfList: {description: "Equivalent to gffcompare's `-i` option.", category: "advanced"}
+ # inputs
inputGtfFiles: {description: "The input GTF files.", category: "required"}
referenceAnnotation: {description: "The GTF file to compare with.", category: "required"}
- outputDir: {description: "The location the output should be written.", category: "common"}
outPrefix: {description: "The prefix for the output.", category: "advanced"}
- genomeSequences: {description: "Equivalent to gffcompare's `-s` option.", category: "advanced"}
- maxDistanceFreeEndsTerminalExons: {description: "Equivalent to gffcompare's `-e` option.", category: "advanced"}
- maxDistanceGroupingTranscriptStartSites: {description: "Equivalent to gffcompare's `-d` option.", category: "advanced"}
- namePrefix: {description: "Equivalent to gffcompare's `-p` option.", category: "advanced"}
C: {description: "Equivalent to gffcompare's `-C` flag.", category: "advanced"}
A: {description: "Equivalent to gffcompare's `-A` flag.", category: "advanced"}
X: {description: "Equivalent to gffcompare's `-X` flag.", category: "advanced"}
@@ -137,9 +136,24 @@ task GffCompare {
noTmap: {description: "Equivalent to gffcompare's `-T` flag.", category: "advanced"}
verbose: {description: "Equivalent to gffcompare's `-V` flag.", category: "advanced"}
debugMode: {description: "Equivalent to gffcompare's `-D` flag.", category: "advanced"}
+ inputGtfList: {description: "Equivalent to gffcompare's `-i` option.", category: "advanced"}
+ outputDir: {description: "The location the output should be written.", category: "common"}
+ genomeSequences: {description: "Equivalent to gffcompare's `-s` option.", category: "advanced"}
+ maxDistanceFreeEndsTerminalExons: {description: "Equivalent to gffcompare's `-e` option.", category: "advanced"}
+ maxDistanceGroupingTranscriptStartSites: {description: "Equivalent to gffcompare's `-d` option.", category: "advanced"}
+ namePrefix: {description: "Equivalent to gffcompare's `-p` option.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ annotated: {description: "Annotated GTF file."}
+ loci: {description: "File describing the processed loci."}
+ stats: {description: "Various statistics related to the “accuracy” (or a measure of agreement) of the input transcripts when compared to reference annotation data."}
+ tracking: {description: "File matching up transcripts between samples."}
+ allFiles: {description: "A collection of all output files."}
+ redundant: {description: "File containing duplicate/redundant transcripts."}
+ missedIntrons: {description: "File denoting missed introns."}
}
meta {
@@ -147,4 +161,4 @@ task GffCompare {
exclude: ["noneFile"]
}
}
-}
\ No newline at end of file
+}
diff --git a/gffread.wdl b/gffread.wdl
index d83e4d76..26a2773c 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -24,19 +24,22 @@ task GffRead {
input {
File inputGff
File genomicSequence
+ Boolean outputGtfFormat = false
+
File? genomicIndex # Optional. GFFRead can create this by itself.
String? exonsFastaPath
String? CDSFastaPath
String? proteinFastaPath
String? filteredGffPath
- Boolean outputGtfFormat = false
- Int timeMinutes = 1 + ceil(size(inputGff) * 10)
+
+ String memory = "4GiB"
+ Int timeMinutes = 1 + ceil(size(inputGff, "GiB") * 10)
String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
}
# The mkdirs below are hackish. It should be
- # ~{"mkir -p $(dirname " + somePath + ")"}
- # but this goes wrong. Cromwell will always use ')' even if somepath is not defined.
+ # ~{"mkir -p $(dirname " + somePath + ")"} but this goes wrong.
+ # Cromwell will always use ')' even if somepath is not defined.
# Which leads to crashing.
command {
set -e
@@ -62,21 +65,29 @@ task GffRead {
}
runtime {
- docker: dockerImage
+ memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputGff: {description: "The input GFF file.", category: "required"}
genomicSequence: {description: "The genome.", category: "required"}
+ outputGtfFormat: {description: "Equivalent to gffread's `-T` flag.", category: "advanced"}
genomicIndex: {description: "The genome's index.", category: "advanced"}
exonsFastaPath: {description: "The location the exons fasta should be written to.", category: "advanced"}
CDSFastaPath: {description: "The location the CDS fasta should be written to.", category: "advanced"}
proteinFastaPath: {description: "The location the protein fasta should be written to.", category: "advanced"}
filteredGffPath: {description: "The location the filtered GFF should be written to.", category: "advanced"}
- outputGtfFormat: {description: "Equivalent to gffread's `-T` flag.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ exonsFasta: {description: "Fasta file containing exons."}
+ CDSFasta: {description: "Fasta file containing CDS's."}
+ proteinFasta: {description: "Fasta file containing proteins."}
+ filteredGff: {description: "Filtered GFF file."}
}
-}
\ No newline at end of file
+}
diff --git a/gridss.wdl b/gridss.wdl
new file mode 100644
index 00000000..5aca3825
--- /dev/null
+++ b/gridss.wdl
@@ -0,0 +1,496 @@
+version 1.0
+
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import "bwa.wdl" as bwa
+
+task AnnotateInsertedSequence {
+ input {
+ File inputVcf
+ String outputPath = "gridss.annotated.vcf.gz"
+ File viralReference
+ File viralReferenceFai
+ File viralReferenceDict
+ File viralReferenceImg
+
+ Int threads = 8
+ String javaXmx = "8G"
+ String memory = "9GiB"
+ String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+ Int timeMinutes = 120
+ }
+
+ command {
+ set -e
+ _JAVA_OPTIONS="$_JAVA_OPTIONS -Xmx~{javaXmx}"
+ AnnotateInsertedSequence \
+ REFERENCE_SEQUENCE=~{viralReference} \
+ INPUT=~{inputVcf} \
+ OUTPUT=~{outputPath} \
+ ALIGNMENT=APPEND \
+ WORKING_DIR='.' \
+ WORKER_THREADS=~{threads}
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputVcf: {description: "The input VCF file.", category: "required"}
+ outputPath: {description: "The path the output will be written to.", category: "common"}
+ viralReference: {description: "A fasta file with viral sequences.", category: "required"}
+ viralReferenceFai: {description: "The index for the viral reference fasta.", category: "required"}
+ viralReferenceDict: {description: "The dict file for the viral reference.", category: "required"}
+ viralReferenceImg: {description: "The BWA index image (generated with GATK BwaMemIndexImageCreator) of the viral reference.", category: "required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task AnnotateSvTypes {
+ input {
+ File gridssVcf
+ File gridssVcfIndex
+ String outputPath = "./gridss.svtyped.vcf.bgz"
+
+ String memory = "32GiB"
+ String dockerImage = "quay.io/biocontainers/bioconductor-structuralvariantannotation:1.10.0--r41hdfd78af_0"
+ Int timeMinutes = 240
+ }
+
+ String effectiveOutputPath = sub(outputPath, "\\.bgz", "")
+ String index = if effectiveOutputPath != outputPath then "T" else "F"
+
+
+ # Based on https://github.com/PapenfussLab/gridss/issues/74
+ command <<<
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ R --vanilla << "EOF"
+ library(VariantAnnotation)
+ library(StructuralVariantAnnotation)
+
+ vcf_path <- "~{gridssVcf}"
+ out_path <- "~{effectiveOutputPath}"
+
+ # Simple SV type classifier
+ simpleEventType <- function(gr) {
+ return(ifelse(seqnames(gr) != seqnames(partner(gr)), "BND", # inter-chromosomosal
+ ifelse(gr$insLen >= abs(gr$svLen) * 0.7, "INS",
+ ifelse(strand(gr) == strand(partner(gr)), "INV",
+ ifelse(xor(start(gr) < start(partner(gr)), strand(gr) == "-"), "DEL",
+ "DUP")))))
+ }
+
+ header <- scanVcfHeader(vcf_path)
+ vcf <- readVcf(vcf_path, seqinfo(header))
+ gr <- breakpointRanges(vcf)
+ svtype <- simpleEventType(gr)
+ info(vcf[gr$sourceId])$SVTYPE <- svtype
+ # GRIDSS doesn't supply a GT, simply set it to 0/1
+ geno(vcf)$GT <- as.matrix(sapply(row.names(vcf), function(x) {"0/1"}))
+ # Select only one breakend per event (also removes single breakends):
+ # sourceId ends with o or h for paired breakends, the first in the pair
+ # end with o the second with h. Single breakend end with b, these will
+ # also be removed since we can't determine the SVTYPE.
+ gr2 <- gr[grepl(".*o$", gr$sourceId)]
+ writeVcf(vcf[gr2$sourceId], out_path, index=~{index})
+ EOF
+ >>>
+
+ output {
+ File vcf = outputPath
+ File? vcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ gridssVcf: {description: "The VCF produced by GRIDSS.", category: "required"}
+ gridssVcfIndex: {description: "The index for the VCF produced by GRIDSS.", category: "required"}
+ outputPath: {description: "The path the output should be written to.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task FilterPon {
+ input {
+ File ponBed
+ File ponBedpe
+ Int minimumScore = 3
+ String outputDir = "."
+
+ String memory = "1GiB"
+ String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+ Int timeMinutes = 20
+ }
+
+ command <<<
+ set -e
+ mkdir -p ~{outputDir}
+
+ cat ~{ponBed} | awk '{if ($5 >= ~{minimumScore}) print $0}' > ~{outputDir}/gridss_pon_single_breakend.bed
+ cat ~{ponBedpe} | awk '{if ($8 >= ~{minimumScore}) print $0}' > ~{outputDir}/gridss_pon_breakpoint.bedpe
+ >>>
+
+ output {
+ File bedpe = "~{outputDir}/gridss_pon_breakpoint.bedpe"
+ File bed = "~{outputDir}/gridss_pon_single_breakend.bed"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ ponBed: {description: "The PON BED file.", category: "required"}
+ ponBedpe: {description: "The PON BEDPE file.", category: "required"}
+ minimumScore: {description: "The minimum number normal samples an SV must have been found in to be kept.", category: "advanced"}
+ outputDir: {description: "The directory the output will be written to.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task GeneratePonBedpe {
+ input {
+ Array[File]+ vcfFiles
+ Array[File]+ vcfIndexes
+ File referenceFasta
+ File referenceFastaFai
+ String outputDir = "."
+
+ Int threads = 8
+ String javaXmx = "8G"
+ String memory = "9GiB"
+ String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+ Int timeMinutes = 120
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ java -Xmx~{javaXmx} \
+ -cp /usr/local/share/gridss-2.12.2-0/gridss.jar \
+ gridss.GeneratePonBedpe \
+ INPUT=~{sep=" INPUT=" vcfFiles} \
+ NO=0 \
+ O=~{outputDir}/gridss_pon_breakpoint.bedpe \
+ SBO=~{outputDir}/gridss_pon_single_breakend.bed \
+ REFERENCE_SEQUENCE=~{referenceFasta} \
+ THREADS=~{threads}
+ }
+
+ output {
+ File bedpe = "~{outputDir}/gridss_pon_breakpoint.bedpe"
+ File bed = "~{outputDir}/gridss_pon_single_breakend.bed"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ vcfFiles: {description: "The vcf files with the normals as the first sample.", category: "required"}
+ referenceFasta: {description: "The fasta of the reference genome.", category: "required"}
+ referenceFastaFai: {description: "The index for the reference genome fasta.", category: "required"}
+ outputDir: {description: "The directory the output will be written to.", category: "common"}
+ threads: {description: "The number of the threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task GRIDSS {
+ input {
+ Array[File]+ tumorBam
+ Array[File]+ tumorBai
+ Array[String]+ tumorLabel
+ BwaIndex reference
+ String outputPrefix = "gridss"
+
+ File? normalBam
+ File? normalBai
+ String? normalLabel
+ File? blacklistBed
+ File? gridssProperties
+
+ Int jvmHeapSizeGb = 64
+ Int nonJvmMemoryGb = 10
+ Int threads = 12
+ Int timeMinutes = ceil(7200 / threads) + 1800
+ String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ gridss \
+ -w . \
+ --reference ~{reference.fastaFile} \
+ --output ~{outputPrefix}.vcf.gz \
+ --assembly ~{outputPrefix}_assembly.bam \
+ ~{"-c " + gridssProperties} \
+ ~{"-t " + threads} \
+ ~{"--jvmheap " + jvmHeapSizeGb + "G"} \
+ --labels ~{normalLabel}~{true="," false="" defined(normalLabel)}~{sep="," tumorLabel} \
+ ~{"--blacklist " + blacklistBed} \
+ ~{normalBam} \
+ ~{sep=" " tumorBam}
+ samtools index ~{outputPrefix}_assembly.bam ~{outputPrefix}_assembly.bai
+
+ # For some reason the VCF index is sometimes missing
+ if [ ! -e ~{outputPrefix}.vcf.gz.tbi ]
+ then
+ tabix ~{outputPrefix}.vcf.gz
+ fi
+ }
+
+ output {
+ File vcf = outputPrefix + ".vcf.gz"
+ File vcfIndex = outputPrefix + ".vcf.gz.tbi"
+ File assembly = outputPrefix + "_assembly.bam"
+ File assemblyIndex = outputPrefix + "_assembly.bai"
+ }
+
+ runtime {
+ cpu: threads
+ memory: "~{jvmHeapSizeGb + nonJvmMemoryGb}GiB"
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ tumorBam: {description: "The input BAM file. This should be the tumor/case sample in case of a paired analysis.", category: "required"}
+ tumorBai: {description: "The index for tumorBam.", category: "required"}
+ tumorLabel: {description: "The name of the (tumor) sample.", category: "required"}
+ reference: {description: "A BWA index, this should also include the fasta index file (.fai).", category: "required"}
+ outputPrefix: {description: "The prefix for the output files. This may include parent directories.", category: "common"}
+ normalBam: {description: "The BAM file for the normal/control sample.", category: "advanced"}
+ normalBai: {description: "The index for normalBam.", category: "advanced"}
+ normalLabel: {description: "The name of the normal sample.", category: "advanced"}
+ blacklistBed: {description: "A bed file with blaclisted regins.", category: "advanced"}
+ gridssProperties: {description: "A properties file for gridss.", category: "advanced"}
+
+ threads: {description: "The number of the threads to use.", category: "advanced"}
+ jvmHeapSizeGb: {description: "The size of JVM heap for assembly and variant calling", category: "advanced"}
+ nonJvmMemoryGb: {description: "The amount of memory in Gb to be requested besides JVM memory.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ vcf: {description: "VCF file including variant allele fractions."}
+ vcfIndex: {description: "Index of output VCF."}
+ assembly: {description: "The GRIDSS assembly BAM."}
+ assemblyIndex: {description: "Index of output BAM file."}
+ }
+}
+
+task GridssAnnotateVcfRepeatmasker {
+ input {
+ File gridssVcf
+ File gridssVcfIndex
+ String outputPath = "./gridss.repeatmasker_annotated.vcf.gz"
+
+ String memory = "25GiB"
+ Int threads = 8
+ String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+ Int timeMinutes = 1440
+ }
+
+ command {
+ gridss_annotate_vcf_repeatmasker \
+ --output ~{outputPath} \
+ --jar /usr/local/share/gridss-2.12.2-0/gridss.jar \
+ -w . \
+ -t ~{threads} \
+ ~{gridssVcf}
+ }
+
+ output {
+ File annotatedVcf = outputPath
+ File annotatedVcfIndex = "~{outputPath}.tbi"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ gridssVcf: {description: "The GRIDSS output.", category: "required"}
+ gridssVcfIndex: {description: "The index for the GRIDSS output.", category: "required"}
+ outputPath: {description: "The path the output should be written to.", category: "common"}
+ threads: {description: "The number of the threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task SomaticFilter {
+ input {
+ File vcfFile
+ File vcfIndex
+ File ponBed
+ File ponBedpe
+ String outputPath = "./high_confidence_somatic.vcf"
+ String fullOutputPath = "./high_and_low_confidence_somatic.vcf"
+
+ String memory = "16GiB"
+ String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+ Int timeMinutes = 60
+ }
+
+ String ponDir = sub(ponBed, basename(ponBed), "")
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPath})
+ mkdir -p $(dirname ~{fullOutputPath})
+
+ gridss_somatic_filter \
+ --pondir ~{ponDir} \
+ --input ~{vcfFile} \
+ --output ~{outputPath} \
+ --fulloutput ~{fullOutputPath}
+ }
+
+ output {
+ File fullVcf = "~{fullOutputPath}.bgz"
+ File fullVcfIndex = "~{fullOutputPath}.bgz.tbi"
+ File highConfidenceVcf = "~{outputPath}.bgz"
+ File highConfidenceVcfIndex = "~{outputPath}.bgz.tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ vcfFile: {description: "The GRIDSS VCF file.", category: "required"}
+ vcfIndex: {description: "The index for the GRIDSS VCF file.", category: "required"}
+ ponBed: {description: "The PON BED file.", category: "required"}
+ ponBedpe: {description: "The PON BEDPE file.", category: "required"}
+ outputPath: {description: "The path the high confidence output should be written to.", category: "common"}
+ fullOutputPath: {description: "The path the full output should be written to.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Virusbreakend {
+ input {
+ File bam
+ File bamIndex
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ File referenceImg
+ File virusbreakendDB
+ String outputPath = "./virusbreakend.vcf"
+
+ String memory = "75GiB"
+ Int threads = 12
+ String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+ Int timeMinutes = 320
+ }
+
+ command {
+ set -e
+ mkdir virusbreakenddb
+ tar -xzvf ~{virusbreakendDB} -C virusbreakenddb --strip-components 1
+ virusbreakend \
+ --output ~{outputPath} \
+ --workingdir . \
+ --reference ~{referenceFasta} \
+ --db virusbreakenddb \
+ --jar /usr/local/share/gridss-2.12.2-0/gridss.jar \
+ -t ~{threads} \
+ ~{bam}
+ }
+
+ output {
+ File vcf = outputPath
+ File summary = "~{outputPath}.summary.tsv"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ bam: {description: "A BAM file.", category: "required"}
+ bamIndex: {description: "The index for the BAM file.", category: "required"}
+ referenceFasta: {description: "The fasta of the reference genome.", category: "required"}
+ referenceImg: {description: "The BWA index image (generated with GATK BwaMemIndexImageCreator) of the reference.", category: "required"}
+ virusbreakendDB: {description: "A .tar.gz containing the virusbreakend database.", category: "required"}
+ outputPath: {description: "The path the output should be written to.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ threads: {description: "The number of the threads to use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
diff --git a/hisat2.wdl b/hisat2.wdl
index f9a4bc59..50fabc9d 100644
--- a/hisat2.wdl
+++ b/hisat2.wdl
@@ -22,9 +22,9 @@ version 1.0
task Hisat2 {
input {
- Array[File]+ indexFiles
File inputR1
File? inputR2
+ Array[File]+ indexFiles
String outputBam
String sample
String library
@@ -32,22 +32,22 @@ task Hisat2 {
String platform = "illumina"
Boolean downstreamTranscriptomeAssembly = true
String summaryFilePath = basename(outputBam, ".bam") + ".summary.txt"
-
- Int threads = 4
- Int? sortThreads
Int sortMemoryPerThreadGb = 2
Int compressionLevel = 1
+
+ Int? sortThreads
+
+ Int threads = 4
Int? memoryGb
Int timeMinutes = 1 + ceil(size([inputR1, inputR2], "G") * 180 / threads)
# quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1
- # is a combination of hisat2 and samtools
- # hisat2=2.2.0, samtools=1.10
+ # is a combination of hisat2 and samtools hisat2=2.2.0 & samtools=1.10.
String dockerImage = "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
}
- # Samtools sort may block the pipe while it is writing data to disk.
+ # Samtools sort may block the pipe while it is writing data to disk.
# This can lead to cpu underutilization.
- # 1 thread if threads is 1. For 2-4 threads 2 sort threads. 3 sort threads for 5-8 threads.
+ # 1 thread if threads is 1. For 2-4 threads 2 sort threads. 3 sort threads for 5-8 threads.
Int estimatedSortThreads = if threads == 1 then 1 else 1 + ceil(threads / 4.0)
Int totalSortThreads = select_first([sortThreads, estimatedSortThreads])
Int estimatedMemoryGb = 1 + ceil(size(indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * totalSortThreads
@@ -81,16 +81,17 @@ task Hisat2 {
}
runtime {
- memory: "~{select_first([memoryGb, estimatedMemoryGb])}G"
cpu: threads
+ memory: "~{select_first([memoryGb, estimatedMemoryGb])}GiB"
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- indexFiles: {description: "The hisat2 index files.", category: "required"}
+ # inputs
inputR1: {description: "The first-/single-end FastQ file.", category: "required"}
inputR2: {description: "The second-end FastQ file.", category: "common"}
+ indexFiles: {description: "The hisat2 index files.", category: "required"}
outputBam: {description: "The location the output BAM file should be written to.", category: "required"}
sample: {description: "The sample id.", category: "required"}
library: {description: "The library id.", category: "required"}
@@ -98,13 +99,16 @@ task Hisat2 {
platform: {description: "The platform used for sequencing.", category: "advanced"}
downstreamTranscriptomeAssembly: {description: "Equivalent to hisat2's `--dta` flag.", category: "advanced"}
summaryFilePath: {description: "Where the summary file should be written.", category: "advanced"}
+ sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
+ compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
+ sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
- sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
- sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
- compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ bamFile: {description: "Output BAM file."}
+ summaryFile: {description: "Alignment summary file."}
}
-}
\ No newline at end of file
+}
diff --git a/hmftools.wdl b/hmftools.wdl
new file mode 100644
index 00000000..c27630a1
--- /dev/null
+++ b/hmftools.wdl
@@ -0,0 +1,1368 @@
+version 1.0
+
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Amber {
+ input {
+ String referenceName
+ File referenceBam
+ File referenceBamIndex
+ String tumorName
+ File tumorBam
+ File tumorBamIndex
+ String outputDir = "./amber"
+ File loci
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+
+ Int threads = 2
+ String memory = "85GiB"
+ String javaXmx = "80G"
+ Int timeMinutes = 480
+ String dockerImage = "quay.io/biocontainers/hmftools-amber:3.5--0"
+ }
+
+ command {
+ AMBER -Xmx~{javaXmx} \
+ -reference ~{referenceName} \
+ -reference_bam ~{referenceBam} \
+ -tumor ~{tumorName} \
+ -tumor_bam ~{tumorBam} \
+ -output_dir ~{outputDir} \
+ -threads ~{threads} \
+ -ref_genome ~{referenceFasta} \
+ -loci ~{loci}
+ }
+
+ output {
+ File version = "~{outputDir}/amber.version"
+ File tumorBafPcf = "~{outputDir}/~{tumorName}.amber.baf.pcf"
+ File tumorBafTsv = "~{outputDir}/~{tumorName}.amber.baf.tsv"
+ File tumorBafVcf = "~{outputDir}/~{tumorName}.amber.baf.vcf.gz"
+ File tumorBafVcfIndex = "~{outputDir}/~{tumorName}.amber.baf.vcf.gz.tbi"
+ File tumorContaminationVcf = "~{outputDir}/~{tumorName}.amber.contamination.vcf.gz"
+ File tumorContaminationVcfIndex = "~{outputDir}/~{tumorName}.amber.contamination.vcf.gz.tbi"
+ File tumorContaminationTsv = "~{outputDir}/~{tumorName}.amber.contamination.tsv"
+ File tumorQc = "~{outputDir}/~{tumorName}.amber.qc"
+ File normalSnpVcf = "~{outputDir}/~{referenceName}.amber.snp.vcf.gz"
+ File normalSnpVcfIndex = "~{outputDir}/~{referenceName}.amber.snp.vcf.gz.tbi"
+ Array[File] outputs = [version, tumorBafPcf, tumorBafTsv, tumorBafVcf, tumorBafVcfIndex,
+ tumorContaminationVcf, tumorContaminationVcfIndex, tumorContaminationTsv, tumorQc,
+ normalSnpVcf, normalSnpVcfIndex]
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ cpu: threads
+ }
+
+ parameter_meta {
+ referenceName: {description: "the name of the normal sample.", category: "required"}
+ referenceBam: {description: "The normal BAM file.", category: "required"}
+ referenceBamIndex: {description: "The index for the normal BAM file.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ tumorBam: {description: "The tumor BAM file.", category: "required"}
+ tumorBamIndex: {description: "The index for the tumor BAM file.", category: "required"}
+ outputDir: {description: "The path to the output directory.", category: "common"}
+ loci: {description: "A VCF file containing likely heterozygous sites.", category: "required"}
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ threads: {description: "The number of threads the program will use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Cobalt {
+ input {
+ String referenceName
+ File referenceBam
+ File referenceBamIndex
+ String tumorName
+ File tumorBam
+ File tumorBamIndex
+ String outputDir = "./cobalt"
+ File gcProfile
+
+ Int threads = 1
+ String memory = "5GiB"
+ String javaXmx = "4G"
+ Int timeMinutes = 480
+ String dockerImage = "quay.io/biocontainers/hmftools-cobalt:1.11--0"
+ }
+
+ command {
+ COBALT -Xmx~{javaXmx} \
+ -reference ~{referenceName} \
+ -reference_bam ~{referenceBam} \
+ -tumor ~{tumorName} \
+ -tumor_bam ~{tumorBam} \
+ -output_dir ~{outputDir} \
+ -threads ~{threads} \
+ -gc_profile ~{gcProfile}
+ }
+
+ output {
+ File version = "~{outputDir}/cobalt.version"
+ File normalGcMedianTsv = "~{outputDir}/~{referenceName}.cobalt.gc.median.tsv"
+ File normalRationMedianTsv = "~{outputDir}/~{referenceName}.cobalt.ratio.median.tsv"
+ File normalRationPcf = "~{outputDir}/~{referenceName}.cobalt.ratio.pcf"
+ File tumorGcMedianTsv = "~{outputDir}/~{tumorName}.cobalt.gc.median.tsv"
+ File tumorRatioPcf = "~{outputDir}/~{tumorName}.cobalt.ratio.pcf"
+ File tumorRatioTsv = "~{outputDir}/~{tumorName}.cobalt.ratio.tsv"
+ File tumorChrLen = "~{outputDir}/~{tumorName}.chr.len"
+ Array[File] outputs = [version, normalGcMedianTsv, normalRationMedianTsv,
+ normalRationPcf, tumorGcMedianTsv, tumorRatioPcf, tumorRatioTsv, tumorChrLen]
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ cpu: threads
+ }
+
+ parameter_meta {
+ referenceName: {description: "the name of the normal sample.", category: "required"}
+ referenceBam: {description: "The normal BAM file.", category: "required"}
+ referenceBamIndex: {description: "The index for the normal BAM file.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ tumorBam: {description: "The tumor BAM file.", category: "required"}
+ tumorBamIndex: {description: "The index for the tumor BAM file.", category: "required"}
+ outputDir: {description: "The path to the output directory.", category: "common"}
+ gcProfile: {description: "A file describing the GC profile of the reference genome.", category: "required"}
+ threads: {description: "The number of threads the program will use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task CupGenerateReport {
+ input {
+ String sampleName
+ File cupData
+ String outputDir = "./cuppa"
+
+ String memory = "5GiB"
+ Int timeMinutes = 10
+ String dockerImage = "quay.io/biowdl/cuppa:1.6"
+ }
+
+ # This script writes to the directory that the input is located in.
+ # Giving the input directly will cause the script to write in the
+ # locallized input dir, which may cause issues with write permissions
+ # in certain execution engines or backends. We, therefore, make links
+ # to a working directory, and give that directory as input instead.
+ # We can't just use the outputDir directly. This could be an
+ # absolute path in which case the linking might fail due to name
+ # collisions. Outputs are copied to the given output dir afterwards.
+ command {
+ set -e
+ mkdir -p ./workdir ~{outputDir}
+ ln -s -t workdir ~{cupData}
+ CupGenerateReport \
+ ~{sampleName} \
+ workdir/
+ mv -t ~{outputDir} \
+ ./workdir/~{sampleName}.cup.report.summary.png \
+ ./workdir/~{sampleName}_cup_report.pdf
+ if [ -f ./workdir/~{sampleName}.cup.report.features.png ]
+ then
+ mv -t ~{outputDir} \
+ ./workdir/~{sampleName}.cup.report.features.png
+ fi
+ }
+
+ output {
+ File summaryPng = "~{outputDir}/~{sampleName}.cup.report.summary.png"
+ File? featuresPng = "~{outputDir}/~{sampleName}.cup.report.features.png"
+ File reportPdf = "~{outputDir}/~{sampleName}_cup_report.pdf"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ sampleName: {description: "The sample id.", category: "required"}
+ cupData: {description: "The output produced by cuppa.", category: "required"}
+ outputDir: {description: "The directory the ouput will be placed in.", category: "common"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Cuppa {
+ input {
+ Array[File]+ linxOutput
+ Array[File]+ purpleOutput
+ String sampleName
+ Array[String]+ categories = ["DNA"]
+ Array[File]+ referenceData
+ File purpleSvVcf
+ File purpleSvVcfIndex
+ File purpleSomaticVcf
+ File purpleSomaticVcfIndex
+ String outputDir = "./cuppa"
+
+ String javaXmx = "4G"
+ String memory = "5GiB"
+ Int timeMinutes = 10
+ String dockerImage = "quay.io/biowdl/cuppa:1.6"
+ }
+
+ command {
+ set -e
+ mkdir -p sampleData ~{outputDir}
+ ln -s -t sampleData ~{sep=" " linxOutput} ~{sep=" " purpleOutput}
+ cuppa -Xmx~{javaXmx} \
+ -output_dir ~{outputDir} \
+ -output_id ~{sampleName} \
+ -categories '~{sep="," categories}' \
+ -ref_data_dir ~{sub(referenceData[0], basename(referenceData[0]), "")} \
+ -sample_data_dir sampleData \
+ -sample_data ~{sampleName} \
+ -sample_sv_file ~{purpleSvVcf} \
+ -sample_somatic_vcf ~{purpleSomaticVcf}
+ }
+
+ output {
+ File cupData = "~{outputDir}/~{sampleName}.cup.data.csv"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ linxOutput: {description: "The files produced by linx.", category: "required"}
+ purpleOutput: {description: "The files produced by purple.", category: "required"}
+ sampleName: {description: "The name of the sample.", category: "required"}
+ categories: {description: "The classifiers to use.", category: "advanced"}
+ referenceData : {description: "The reference data.", category: "required"}
+ purpleSvVcf: {description: "The VCF file produced by purple which contains structural variants.", category: "required"}
+ purpleSvVcfIndex: {description: "The index of the structural variants VCF file produced by purple.", category: "required"}
+ purpleSomaticVcf: {description: "The VCF file produced by purple which contains somatic variants.", category: "required"}
+ purpleSomaticVcfIndex: {description: "The index of the somatic VCF file produced by purple.", category: "required"}
+ outputDir: {description: "The directory the ouput will be placed in.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task CuppaChart {
+ input {
+ String sampleName
+ File cupData
+ String outputDir = "./cuppa"
+
+ String memory = "4GiB"
+ Int timeMinutes = 5
+ String dockerImage = "quay.io/biowdl/cuppa:1.6"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ cuppa-chart \
+ -sample ~{sampleName} \
+ -sample_data ~{cupData} \
+ -output_dir ~{outputDir}
+ }
+
+ output {
+ File cuppaChart = "~{outputDir}/~{sampleName}.cuppa.chart.png"
+ File cuppaConclusion = "~{outputDir}/~{sampleName}.cuppa.conclusion.txt"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ sampleName: {description: "The name of the sample.", category:"common"}
+ cupData: {description: "The cuppa output.", category: "required"}
+ outputDir: {description: "The directory the output will be written to.", category:"common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Gripss {
+ input {
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ File knownFusionPairBedpe
+ File breakendPon
+ File breakpointPon
+ String referenceName
+ String tumorName
+ File vcf
+ File vcfIndex
+ String outputDir = "./"
+
+ String memory = "17GiB"
+ String javaXmx = "16G"
+ Int timeMinutes = 50
+ String dockerImage = "quay.io/biocontainers/hmftools-gripss:2.0--hdfd78af_0"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ gripss -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -ref_genome ~{referenceFasta} \
+ -known_hotspot_file ~{knownFusionPairBedpe} \
+ -pon_sgl_file ~{breakendPon} \
+ -pon_sv_file ~{breakpointPon} \
+ -reference ~{referenceName} \
+ -sample ~{tumorName} \
+ -vcf ~{vcf} \
+ -output_dir ~{outputDir} \
+ -output_id somatic
+ }
+
+ output {
+ File fullVcf = "~{outputDir}/~{tumorName}.gripss.somatic.vcf.gz"
+ File fullVcfIndex = "~{outputDir}/~{tumorName}.gripss.somatic.vcf.gz.tbi"
+ File filteredVcf = "~{outputDir}/~{tumorName}.gripss.filtered.somatic.vcf.gz"
+ File filteredVcfIndex = "~{outputDir}/~{tumorName}.gripss.filtered.somatic.vcf.gz.tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ knownFusionPairBedpe: {description: "Equivalent to the `-known_hotspot_file` option.", category: "required"}
+ breakendPon: {description: "Equivalent to the `-pon_sgl_file` option.", category: "required"}
+ breakpointPon: {description: "Equivalent to the `-pon_sv_file` option.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
+ vcf: {description: "The input VCF.", category: "required"}
+ vcfIndex: {description: "The index for the input VCF.", category: "required"}
+ outputDir: {description: "The path the output will be written to.", category:"required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task GripssApplicationKt {
+ # Obsolete
+ input {
+ File inputVcf
+ String outputPath = "gripss.vcf.gz"
+ String tumorName
+ String referenceName
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ File breakpointHotspot
+ File breakendPon
+ File breakpointPon
+
+ String memory = "32GiB"
+ String javaXmx = "31G"
+ Int timeMinutes = 45
+ String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.11--hdfd78af_0"
+ }
+
+ command {
+ java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -cp /usr/local/share/hmftools-gripss-1.11-0/gripss.jar \
+ com.hartwig.hmftools.gripss.GripssApplicationKt \
+ -tumor ~{tumorName} \
+ -reference ~{referenceName} \
+ -ref_genome ~{referenceFasta} \
+ -breakpoint_hotspot ~{breakpointHotspot} \
+ -breakend_pon ~{breakendPon} \
+ -breakpoint_pon ~{breakpointPon} \
+ -input_vcf ~{inputVcf} \
+ -output_vcf ~{outputPath} \
+ -paired_normal_tumor_ordinals
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputVcf: {description: "The input VCF.", category: "required"}
+ outputPath: {description: "The path where th eoutput VCF will be written.", category: "common"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ breakpointHotspot: {description: "Equivalent to the `-breakpoint_hotspot` option.", category: "required"}
+ breakendPon: {description: "Equivalent to the `-breakend_pon` option.", category: "required"}
+ breakpointPon: {description: "Equivalent to the `-breakpoint_pon` option.", category: "required"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task GripssHardFilterApplicationKt {
+ # Obsolete
+ input {
+ File inputVcf
+ String outputPath = "gripss_hard_filter.vcf.gz"
+
+ String memory = "3GiB"
+ String javaXmx = "2G"
+ Int timeMinutes = 15
+ String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.11--hdfd78af_0"
+ }
+
+ command {
+ java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -cp /usr/local/share/hmftools-gripss-1.11-0/gripss.jar \
+ com.hartwig.hmftools.gripss.GripssHardFilterApplicationKt \
+ -input_vcf ~{inputVcf} \
+ -output_vcf ~{outputPath}
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputVcf: {description: "The input VCF.", category: "required"}
+ outputPath: {description: "The path where th eoutput VCF will be written.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task HealthChecker {
+ input {
+ String outputDir = "."
+ String referenceName
+ File referenceFlagstats
+ File referenceMetrics
+ String tumorName
+ File tumorFlagstats
+ File tumorMetrics
+ Array[File]+ purpleOutput
+
+ String javaXmx = "2G"
+ String memory = "3GiB"
+ Int timeMinutes = 1
+ String dockerImage = "quay.io/biowdl/health-checker:3.2"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ health-checker -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -reference ~{referenceName} \
+ -ref_flagstat_file ~{referenceFlagstats} \
+ -ref_wgs_metrics_file ~{referenceMetrics} \
+ -tumor ~{tumorName} \
+ -tum_flagstat_file ~{tumorFlagstats} \
+ -tum_wgs_metrics_file ~{tumorMetrics} \
+ -purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \
+ -output_dir ~{outputDir}
+ if [ -e '~{outputDir}/~{tumorName}.HealthCheckSucceeded' ]
+ then
+ echo 'true' > '~{outputDir}/succeeded'
+ fi
+ if [ -e '~{outputDir}/~{tumorName}.HealthCheckFailed' ]
+ then
+ echo 'false' > '~{outputDir}/succeeded'
+ fi
+ }
+
+ output {
+ Boolean succeeded = read_boolean("succeeded")
+ File outputFile = if succeeded
+ then "~{outputDir}/~{tumorName}.HealthCheckSucceeded"
+ else "~{outputDir}/~{tumorName}.HealthCheckFailed"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ outputDir: {description: "The path the output will be written to.", category:"required"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
+ referenceFlagstats: {description: "The flagstats for the normal sample.", category: "required"}
+ referenceMetrics: {description: "The picard WGS metrics for the normal sample.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ tumorFlagstats: {description: "The flagstats for the tumor sample.", category: "required"}
+ tumorMetrics: {description: "The picard WGS metrics for the tumor sample.", category: "required"}
+ purpleOutput: {description: "The files from purple's output directory.", category: "required"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Linx {
+ input {
+ String sampleName
+ File svVcf
+ File svVcfIndex
+ Array[File]+ purpleOutput
+ String refGenomeVersion
+ String outputDir = "./linx"
+ File fragileSiteCsv
+ File lineElementCsv
+ File knownFusionCsv
+ File driverGenePanel
+ Boolean writeAllVisFusions = false
+ #The following should be in the same directory.
+ File geneDataCsv
+ File proteinFeaturesCsv
+ File transExonDataCsv
+ File transSpliceDataCsv
+
+ String memory = "9GiB"
+ String javaXmx = "8G"
+ Int timeMinutes = 10
+ String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
+ }
+
+ command {
+ linx -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -sample ~{sampleName} \
+ -sv_vcf ~{svVcf} \
+ -purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \
+ -ref_genome_version ~{refGenomeVersion} \
+ -output_dir ~{outputDir} \
+ -fragile_site_file ~{fragileSiteCsv} \
+ -line_element_file ~{lineElementCsv} \
+ -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
+ -check_fusions \
+ -known_fusion_file ~{knownFusionCsv} \
+ -check_drivers \
+ -driver_gene_panel ~{driverGenePanel} \
+ -chaining_sv_limit 0 \
+ -write_vis_data \
+ ~{if writeAllVisFusions then "-write_all_vis_fusions" else ""}
+ }
+
+ output {
+ File driverCatalog = "~{outputDir}/~{sampleName}.linx.driver.catalog.tsv"
+ File linxBreakend = "~{outputDir}/~{sampleName}.linx.breakend.tsv"
+ File linxClusters = "~{outputDir}/~{sampleName}.linx.clusters.tsv"
+ File linxDrivers = "~{outputDir}/~{sampleName}.linx.drivers.tsv"
+ File linxFusion = "~{outputDir}/~{sampleName}.linx.fusion.tsv"
+ File linxLinks = "~{outputDir}/~{sampleName}.linx.links.tsv"
+ File linxSvs = "~{outputDir}/~{sampleName}.linx.svs.tsv"
+ File linxVisCopyNumber = "~{outputDir}/~{sampleName}.linx.vis_copy_number.tsv"
+ File linxVisFusion = "~{outputDir}/~{sampleName}.linx.vis_fusion.tsv"
+ File linxVisGeneExon = "~{outputDir}/~{sampleName}.linx.vis_gene_exon.tsv"
+ File linxVisProteinDomain = "~{outputDir}/~{sampleName}.linx.vis_protein_domain.tsv"
+ File linxVisSegments = "~{outputDir}/~{sampleName}.linx.vis_segments.tsv"
+ File linxVisSvData = "~{outputDir}/~{sampleName}.linx.vis_sv_data.tsv"
+ File linxVersion = "~{outputDir}/linx.version"
+ Array[File] outputs = [driverCatalog, linxBreakend, linxClusters, linxDrivers, linxFusion,
+ linxLinks, linxSvs, linxVisCopyNumber, linxVisFusion,
+ linxVisGeneExon, linxVisProteinDomain, linxVisSegments, linxVisSvData,
+ linxVersion]
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ sampleName: {description: "The name of the sample.", category: "required"}
+ svVcf: {description: "A VCF file containing structural variants, produced using GRIDSS, annotated for viral insertions and postprocessed with GRIPSS.", category: "required"}
+ svVcfIndex: {description: "Index for the structural variants VCf file.", category: "required"}
+ purpleOutput: {description: "The files produced by PURPLE.", category: "required"}
+ refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
+ outputDir: {description: "The directory the outputs will be written to.", category: "required"}
+ fragileSiteCsv: {description: "A list of known fragile sites.", category: "required"}
+ lineElementCsv: {description: "A list of known LINE source regions.", category: "required"}
+ knownFusionCsv: {description: "A CSV file describing known fusions.", category: "required"}
+ driverGenePanel: {description: "A TSV file describing the driver gene panel.", category: "required"}
+ writeAllVisFusions: {description: "Equivalent to the -write_all_vis_fusions flag.", category: "advanced"}
+ geneDataCsv: {description: "A CSV file containing gene information, must be in the same directory as `proteinFeaturesCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ proteinFeaturesCsv: {description: "A CSV file containing protein feature information, must be in the same directory as `geneDataCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ transExonDataCsv: {description: "A CSV file containing transcript exon information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transSpliceDataCsv`.", category: "required"}
+ transSpliceDataCsv: {description: "A CSV file containing transcript splicing information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transExonDataCsv`.", category: "required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task LinxVisualisations {
+ input {
+ String outputDir = "./linx_visualisation"
+ String sample
+ String refGenomeVersion
+ Array[File]+ linxOutput
+ Boolean plotReportable = true
+
+ String memory = "9GiB"
+ String javaXmx = "8G"
+ Int timeMinutes = 1440
+ String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -cp /usr/local/share/hmftools-linx-1.18-0/sv-linx.jar \
+ com.hartwig.hmftools.linx.visualiser.SvVisualiser \
+ -sample ~{sample} \
+ -ref_genome_version ~{refGenomeVersion} \
+ -circos /usr/local/bin/circos \
+ -vis_file_dir ~{sub(linxOutput[0], basename(linxOutput[0]), "")} \
+ -data_out ~{outputDir}/circos \
+ -plot_out ~{outputDir}/plots \
+ ~{if plotReportable then "-plot_reportable" else ""}
+ }
+
+ output {
+ Array[File] circos = glob("~{outputDir}/circos/*")
+ Array[File] plots = glob("~{outputDir}/plots/*")
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ outputDir: {description: "The directory the outputs will be written to.", category: "required"}
+ sample: {description: "The sample's name.", category: "required"}
+ refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
+ linxOutput: {description: "The directory containing the linx output.", category: "required"}
+ plotReportable: {description: "Equivalent to the -plot_reportable flag.", category: "advanced"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Orange {
+ input {
+ String outputDir = "./orange"
+ File doidJson
+ Array[String] sampleDoids
+ String tumorName
+ String referenceName
+ File referenceMetrics
+ File tumorMetrics
+ File referenceFlagstats
+ File tumorFlagstats
+ File sageGermlineGeneCoverageTsv
+ File sageSomaticRefSampleBqrPlot
+ File sageSomaticTumorSampleBqrPlot
+ File purpleGeneCopyNumberTsv
+ File purpleGermlineDriverCatalogTsv
+ File purpleGermlineVariantVcf
+ File purpleGermlineVariantVcfIndex
+ Array[File]+ purplePlots
+ File purplePurityTsv
+ File purpleQcFile
+ File purpleSomaticDriverCatalogTsv
+ File purpleSomaticVariantVcf
+ File purpleSomaticVariantVcfIndex
+ File linxFusionTsv
+ File linxBreakendTsv
+ File linxDriverCatalogTsv
+ File linxDriverTsv
+ Array[File]+ linxPlots
+ File cuppaResultCsv
+ File cuppaSummaryPlot
+ File? cuppaFeaturePlot
+ File chordPredictionTxt
+ File peachGenotypeTsv
+ File protectEvidenceTsv
+ File annotatedVirusTsv
+ #File pipelineVersionFile
+ File cohortMappingTsv
+ File cohortPercentilesTsv
+
+ String memory = "17GiB"
+ String javaXmx = "16G"
+ Int timeMinutes = 10
+ String dockerImage = "quay.io/biowdl/orange:v1.6"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ orange -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -output_dir ~{outputDir} \
+ -doid_json ~{doidJson} \
+ -primary_tumor_doids '~{sep=";" sampleDoids}' \
+ -max_evidence_level C \
+ -tumor_sample_id ~{tumorName} \
+ -reference_sample_id ~{referenceName} \
+ -ref_sample_wgs_metrics_file ~{referenceMetrics} \
+ -tumor_sample_wgs_metrics_file ~{tumorMetrics} \
+ -ref_sample_flagstat_file ~{referenceFlagstats} \
+ -tumor_sample_flagstat_file ~{tumorFlagstats} \
+ -sage_germline_gene_coverage_tsv ~{sageGermlineGeneCoverageTsv} \
+ -sage_somatic_ref_sample_bqr_plot ~{sageSomaticRefSampleBqrPlot} \
+ -sage_somatic_tumor_sample_bqr_plot ~{sageSomaticTumorSampleBqrPlot} \
+ -purple_gene_copy_number_tsv ~{purpleGeneCopyNumberTsv} \
+ -purple_germline_driver_catalog_tsv ~{purpleGermlineDriverCatalogTsv} \
+ -purple_germline_variant_vcf ~{purpleGermlineVariantVcf} \
+ -purple_plot_directory ~{sub(purplePlots[0], basename(purplePlots[0]), "")} \
+ -purple_purity_tsv ~{purplePurityTsv} \
+ -purple_qc_file ~{purpleQcFile} \
+ -purple_somatic_driver_catalog_tsv ~{purpleSomaticDriverCatalogTsv} \
+ -purple_somatic_variant_vcf ~{purpleSomaticVariantVcf} \
+ -linx_fusion_tsv ~{linxFusionTsv} \
+ -linx_breakend_tsv ~{linxBreakendTsv} \
+ -linx_driver_catalog_tsv ~{linxDriverCatalogTsv} \
+ -linx_driver_tsv ~{linxDriverTsv} \
+ -linx_plot_directory ~{sub(linxPlots[0], basename(linxPlots[0]), "")} \
+ -cuppa_result_csv ~{cuppaResultCsv} \
+ -cuppa_summary_plot ~{cuppaSummaryPlot} \
+ ~{"-cuppa_feature_plot " + cuppaFeaturePlot} \
+ -chord_prediction_txt ~{chordPredictionTxt} \
+ -peach_genotype_tsv ~{peachGenotypeTsv} \
+ -protect_evidence_tsv ~{protectEvidenceTsv} \
+ -annotated_virus_tsv ~{annotatedVirusTsv} \
+ -cohort_mapping_tsv ~{cohortMappingTsv} \
+ -cohort_percentiles_tsv ~{cohortPercentilesTsv}
+ }
+ #TODO may need to be added: -pipeline_version_file ~{pipelineVersionFile}
+
+ output {
+ File orangeJson = "~{outputDir}/~{tumorName}.orange.json"
+ File orangePdf = "~{outputDir}/~{tumorName}.orange.pdf"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ outputDir: {description: "The directory the outputs will be written to.", category: "common"}
+ doidJson: {description: "A json with the DOID (Human Disease Ontology) tree.", category: "required"}
+ sampleDoids: {description: "The DOIDs (Human Disease Ontology) for the primary tumor.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
+ referenceMetrics: {description: "The picard WGS metrics for the normal sample.", category: "required"}
+ tumorMetrics: {description: "The picard WGS metrics for the tumor sample.", category: "required"}
+ referenceFlagstats: {description: "The flagstats for the normal sample.", category: "required"}
+ tumorFlagstats: {description: "The flagstats for the tumor sample.", category: "required"}
+ sageGermlineGeneCoverageTsv: {description: "Gene coverage file produced by the germline sage run.", category: "required"}
+ sageSomaticRefSampleBqrPlot: {description: "The reference bqr plot produced by the somatic sage run.", category: "required"}
+ sageSomaticTumorSampleBqrPlot: {description: "The reference bqr plot produced by the somatic sage run.", category: "required"}
+ purpleGeneCopyNumberTsv: {description: "Copy number tsv produced by purple.", category: "required"}
+ purpleGermlineDriverCatalogTsv: {description: "Germline driver catalog produced by purple.", category: "required"}
+ purpleGermlineVariantVcf: {description: "Germline variant vcf produced by purple.", category: "required"}
+ purplePlots: {description: "The plots generated by purple.", category: "required"}
+ purplePurityTsv: {description: "The purity file produced by purple.", category: "required"}
+ purpleQcFile: {description: "The qc file produced by purple.", category: "required"}
+ purpleSomaticDriverCatalogTsv: {description: "Somatic driver catalog produced by purple.", category: "required"}
+ purpleSomaticVariantVcf: {description: "Somatic variant vcf produced by purple.", category: "required"}
+ linxFusionTsv: {description: "The fusions tsv produced by linx.", category: "required"}
+ linxBreakendTsv: {description: "The breakend tsv produced by linx.", category: "required"}
+ linxDriverCatalogTsv: {description: "The driver catalog produced by linx.", category: "required"}
+ linxDriverTsv: {description: "The driver tsv produced by linx.", category: "required"}
+ linxPlots: {description: "The plots generated by linx.", category: "required"}
+ cuppaResultCsv: {description: "The cuppa results csv.", category: "required"}
+ cuppaSummaryPlot: {description: "The cuppa summary plot.", category: "required"}
+ cuppaFeaturePlot: {description: "The cuppa feature plot.", category: "common"}
+ chordPredictionTxt: {description: "Chord prediction results.", category: "required"}
+ peachGenotypeTsv: {description: "Genotype tsv produced by peach.", category: "required"}
+ protectEvidenceTsv: {description: "Evidence tsv produced by protect.", category: "required"}
+ annotatedVirusTsv: {description: "Annotated virus tsv produced by virus-interpreter.", category: "required"}
+ #pipelineVersionFile: {description: "", category: "required"}
+ cohortMappingTsv: {description: "Cohort mapping file from the HMFTools resources.", category: "required"}
+ cohortPercentilesTsv: {description: "Cohort percentile file from the HMFTools resources.", category: "required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Pave {
+ input {
+ String outputDir = "./"
+ String sampleName
+ File vcfFile
+ File vcfFileIndex
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ String refGenomeVersion
+ File driverGenePanel
+ #The following should be in the same directory.
+ File geneDataCsv
+ File proteinFeaturesCsv
+ File transExonDataCsv
+ File transSpliceDataCsv
+
+ Int timeMinutes = 50
+ String javaXmx = "8G"
+ String memory = "9GiB"
+ String dockerImage = "quay.io/biowdl/pave:v1.0"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ pave -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -sample ~{sampleName} \
+ -vcf_file ~{vcfFile} \
+ -output_dir ~{outputDir} \
+ -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
+ -ref_genome ~{referenceFasta} \
+ -ref_genome_version ~{refGenomeVersion} \
+ -driver_gene_panel ~{driverGenePanel}
+ }
+
+ output {
+ File outputVcf = "~{outputDir}/~{sub(basename(vcfFile), 'vcf.gz$', 'pave.vcf.gz')}"
+ File outputVcfIndex = "~{outputDir}/~{sub(basename(vcfFile), 'vcf.gz$', 'pave.vcf.gz.tbi')}"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ outputDir: {description: "The directory the outputs will be written to.", category: "required"}
+ sampleName: {description: "The name of the sample.", category: "required"}
+ vcfFile: {description: "The input VCF file.", category: "required"}
+ vcfFileIndex: {description: "The index for the input vcf file.", category: "required"}
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"HG19\" or \"HG38\".", category: "required"}
+ driverGenePanel: {description: "A TSV file describing the driver gene panel.", category: "required"}
+ geneDataCsv: {description: "A CSV file containing gene information, must be in the same directory as `proteinFeaturesCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ proteinFeaturesCsv: {description: "A CSV file containing protein feature information, must be in the same directory as `geneDataCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ transExonDataCsv: {description: "A CSV file containing transcript exon information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transSpliceDataCsv`.", category: "required"}
+ transSpliceDataCsv: {description: "A CSV file containing transcript splicing information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transExonDataCsv`.", category: "required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Protect {
+ input {
+ String refGenomeVersion
+ String tumorName
+ String referenceName
+ Array[String]+ sampleDoids
+ String outputDir = "."
+ Array[File]+ serveActionability
+ File doidJson
+ File purplePurity
+ File purpleQc
+ File purpleDriverCatalogSomatic
+ File purpleDriverCatalogGermline
+ File purpleSomaticVariants
+ File purpleSomaticVariantsIndex
+ File purpleGermlineVariants
+ File purpleGermlineVariantsIndex
+ File purpleGeneCopyNumber
+ File linxFusion
+ File linxBreakend
+ File linxDriversCatalog
+ File chordPrediction
+ File annotatedVirus
+
+ String memory = "9GiB"
+ String javaXmx = "8G"
+ Int timeMinutes = 60
+ String dockerImage = "quay.io/biowdl/protect:v2.0"
+ }
+
+ command {
+ protect -Xmx~{javaXmx} \
+ -ref_genome_version ~{refGenomeVersion} \
+ -tumor_sample_id ~{tumorName} \
+ -reference_sample_id ~{referenceName} \
+ -primary_tumor_doids '~{sep=";" sampleDoids}' \
+ -output_dir ~{outputDir} \
+ -serve_actionability_dir ~{sub(serveActionability[0], basename(serveActionability[0]), "")} \
+ -doid_json ~{doidJson} \
+ -purple_purity_tsv ~{purplePurity} \
+ -purple_qc_file ~{purpleQc} \
+ -purple_somatic_driver_catalog_tsv ~{purpleDriverCatalogSomatic} \
+ -purple_germline_driver_catalog_tsv ~{purpleDriverCatalogGermline} \
+ -purple_somatic_variant_vcf ~{purpleSomaticVariants} \
+ -purple_germline_variant_vcf ~{purpleGermlineVariants} \
+ -purple_gene_copy_number_tsv ~{purpleGeneCopyNumber} \
+ -linx_fusion_tsv ~{linxFusion} \
+ -linx_breakend_tsv ~{linxBreakend} \
+ -linx_driver_catalog_tsv ~{linxDriversCatalog} \
+ -chord_prediction_txt ~{chordPrediction} \
+ -annotated_virus_tsv ~{annotatedVirus}
+ }
+
+ output {
+ File protectTsv = "~{outputDir}/~{tumorName}.protect.tsv"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
+ sampleDoids: {description: "The DOIDs (Human Disease Ontology) for the primary tumor.", category: "required"}
+ outputDir: {description: "The directory the outputs will be written to.", category: "required"}
+ serveActionability: {description: "The actionability files generated by hmftools' serve.", category: "required"}
+ doidJson: {description: "A json with the DOID (Human Disease Ontology) tree.", category: "required"}
+ purplePurity: {description: "The purity file generated by purple.", category: "required"}
+ purpleQc: {description: "The QC file generated by purple.", category: "required"}
+ purpleDriverCatalogSomatic: {description: "The somatic driver catalog generated by purple.", category: "required"}
+ purpleDriverCatalogGermline: {description: "The germline driver catalog generated by purple.", category: "required"}
+ purpleSomaticVariants: {description: "The somatic VCF generated by purple.", category: "required"}
+ purpleSomaticVariantsIndex: {description: "The index for the somatic VCF generated by purple.", category: "required"}
+ purpleGermlineVariants: {description: "The germline VCF generated by purple.", category: "required"}
+ purpleGermlineVariantsIndex: {description: "The index of the germline VCF generated by purple.", category: "required"}
+ purpleGeneCopyNumber: {description: "The gene copy number file generated by purple.", category: "required"}
+ linxFusion: {description: "The fusion file generated by linx.", category: "required"}
+ linxBreakend: {description: "The breakend file generated by linx.", category: "required"}
+ linxDriversCatalog: {description: "The driver catalog generated generated by linx.", category: "required"}
+ chordPrediction: {description: "The chord prediction file.", category: "required"}
+ annotatedVirus: {description: "The virus-interpreter output.", category: "required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Purple {
+ input {
+ String referenceName
+ String tumorName
+ String outputDir = "./purple"
+ Array[File]+ amberOutput
+ Array[File]+ cobaltOutput
+ File gcProfile
+ File somaticVcf
+ File germlineVcf
+ File filteredSvVcf
+ File filteredSvVcfIndex
+ File fullSvVcf
+ File fullSvVcfIndex
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ File driverGenePanel
+ File somaticHotspots
+ File germlineHotspots
+ Float? highlyDiploidPercentage
+ Float? somaticMinPuritySpread
+ #The following should be in the same directory.
+ File geneDataCsv
+ File proteinFeaturesCsv
+ File transExonDataCsv
+ File transSpliceDataCsv
+
+ Int threads = 1
+ Int timeMinutes = 30
+ String memory = "9GiB"
+ String javaXmx = "8G"
+ # clone of quay.io/biocontainers/hmftools-purple:3.2--hdfd78af_0 with 'ln -s /usr/local/lib/libwebp.so.7 /usr/local/lib/libwebp.so.6'
+ String dockerImage = "quay.io/biowdl/hmftools-purple:3.2"
+ }
+
+ command {
+ PURPLE -Xmx~{javaXmx} \
+ -reference ~{referenceName} \
+ -germline_vcf ~{germlineVcf} \
+ -germline_hotspots ~{germlineHotspots} \
+ -tumor ~{tumorName} \
+ -output_dir ~{outputDir} \
+ -amber ~{sub(amberOutput[0], basename(amberOutput[0]), "")} \
+ -cobalt ~{sub(cobaltOutput[0], basename(cobaltOutput[0]), "")} \
+ -gc_profile ~{gcProfile} \
+ -somatic_vcf ~{somaticVcf} \
+ -structural_vcf ~{filteredSvVcf} \
+ -sv_recovery_vcf ~{fullSvVcf} \
+ -circos /usr/local/bin/circos \
+ -ref_genome ~{referenceFasta} \
+ -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
+ -run_drivers \
+ -somatic_hotspots ~{somaticHotspots} \
+ -driver_gene_panel ~{driverGenePanel} \
+ ~{"-highly_diploid_percentage " + highlyDiploidPercentage} \
+ ~{"-somatic_min_purity_spread " + somaticMinPuritySpread} \
+ -threads ~{threads}
+ }
+
+ output {
+ File driverCatalogGermlineTsv = "~{outputDir}/~{tumorName}.driver.catalog.germline.tsv"
+ File driverCatalogSomaticTsv = "~{outputDir}/~{tumorName}.driver.catalog.somatic.tsv"
+ File purpleCnvGeneTsv = "~{outputDir}/~{tumorName}.purple.cnv.gene.tsv"
+ File purpleCnvSomaticTsv = "~{outputDir}/~{tumorName}.purple.cnv.somatic.tsv"
+ File purpleGermlineDeletionTsv = "~{outputDir}/~{tumorName}.purple.germline.deletion.tsv"
+ File purpleGermlineVcf = "~{outputDir}/~{tumorName}.purple.germline.vcf.gz"
+ File purpleGermlineVcfIndex = "~{outputDir}/~{tumorName}.purple.germline.vcf.gz.tbi"
+ File purplePurityRangeTsv = "~{outputDir}/~{tumorName}.purple.purity.range.tsv"
+ File purplePurityTsv = "~{outputDir}/~{tumorName}.purple.purity.tsv"
+ File purpleQc = "~{outputDir}/~{tumorName}.purple.qc"
+ File purpleSegmentTsv = "~{outputDir}/~{tumorName}.purple.segment.tsv"
+ File purpleSomaticClonalityTsv = "~{outputDir}/~{tumorName}.purple.somatic.clonality.tsv"
+ File purpleSomaticHistTsv = "~{outputDir}/~{tumorName}.purple.somatic.hist.tsv"
+ File purpleSomaticVcf = "~{outputDir}/~{tumorName}.purple.somatic.vcf.gz"
+ File purpleSomaticVcfIndex = "~{outputDir}/~{tumorName}.purple.somatic.vcf.gz.tbi"
+ File purpleSvVcf = "~{outputDir}/~{tumorName}.purple.sv.vcf.gz"
+ File purpleSvVcfIndex = "~{outputDir}/~{tumorName}.purple.sv.vcf.gz.tbi"
+ File purpleVersion = "~{outputDir}/purple.version"
+ File circosPlot = "~{outputDir}/plot/~{tumorName}.circos.png"
+ File copynumberPlot = "~{outputDir}/plot/~{tumorName}.copynumber.png"
+ File inputPlot = "~{outputDir}/plot/~{tumorName}.input.png"
+ File mapPlot = "~{outputDir}/plot/~{tumorName}.map.png"
+ File purityRangePlot = "~{outputDir}/plot/~{tumorName}.purity.range.png"
+ File segmentPlot = "~{outputDir}/plot/~{tumorName}.segment.png"
+ File somaticClonalityPlot = "~{outputDir}/plot/~{tumorName}.somatic.clonality.png"
+ File somaticPlot = "~{outputDir}/plot/~{tumorName}.somatic.png"
+ File? somaticRainfallPlot = "~{outputDir}/plot/~{tumorName}.somatic.rainfall.png"
+ File circosNormalRatio = "~{outputDir}/circos/~{referenceName}.ratio.circos"
+ File circosBaf = "~{outputDir}/circos/~{tumorName}.baf.circos"
+ File circosConf = "~{outputDir}/circos/~{tumorName}.circos.conf"
+ File circosCnv = "~{outputDir}/circos/~{tumorName}.cnv.circos"
+ File circosIndel = "~{outputDir}/circos/~{tumorName}.indel.circos"
+ File circosInputConf = "~{outputDir}/circos/~{tumorName}.input.conf"
+ File circosLink = "~{outputDir}/circos/~{tumorName}.link.circos"
+ File circosMap = "~{outputDir}/circos/~{tumorName}.map.circos"
+ File circosTumorRatio = "~{outputDir}/circos/~{tumorName}.ratio.circos"
+ File circosSnp = "~{outputDir}/circos/~{tumorName}.snp.circos"
+ File circosGaps = "~{outputDir}/circos/gaps.txt"
+ Array[File] outputs = [driverCatalogSomaticTsv, purpleCnvGeneTsv,
+ purpleCnvSomaticTsv, purplePurityRangeTsv, purplePurityTsv, purpleQc,
+ purpleSegmentTsv, purpleSomaticClonalityTsv, purpleSomaticHistTsv,
+ purpleSomaticVcf, purpleSomaticVcfIndex, purpleSvVcf, purpleSvVcfIndex,
+ purpleVersion, purpleGermlineVcf, purpleGermlineVcfIndex, driverCatalogGermlineTsv]
+ Array[File] plots = select_all([circosPlot, copynumberPlot, inputPlot, mapPlot, purityRangePlot,
+ segmentPlot, somaticClonalityPlot, somaticPlot, somaticRainfallPlot])
+ Array[File] circos = [circosNormalRatio, circosConf, circosIndel, circosLink,
+ circosTumorRatio, circosGaps, circosBaf, circosCnv, circosInputConf, circosMap,
+ circosSnp]
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ cpu: threads
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ referenceName: {description: "the name of the normal sample.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ outputDir: {description: "The path to the output directory.", category: "common"}
+ amberOutput: {description: "The output files of hmftools amber.", category: "required"}
+ cobaltOutput: {description: "The output files of hmftools cobalt", category: "required"}
+ gcProfile: {description: "A file describing the GC profile of the reference genome.", category: "required"}
+ somaticVcf: {description: "The somatic variant calling results.", category: "required"}
+ germlineVcf: {description: "The germline variant calling results.", category: "required"}
+ filteredSvVcf: {description: "The filtered structural variant calling results.", category: "required"}
+ fullSvVcf: {description: "The unfiltered structural variant calling results.", category: "required"}
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ driverGenePanel: {description: "A TSV file describing the driver gene panel.", category: "required"}
+ somaticHotspots: {description: "A vcf file with hotspot somatic variant sites.", category: "required"}
+ germlineHotspots: {description: "A vcf file with hotspot germline variant sites.", category: "required"}
+ highlyDiploidPercentage: {description: "Equivalent to PURPLE's `-highly_diploid_percentage` option.", category: "advanced"}
+ somaticMinPuritySpread: {description: "Equivalent to PURPLE's `-somatic_min_purity_spread` option.", category: "advanced"}
+ geneDataCsv: {description: "A CSV file containing gene information, must be in the same directory as `proteinFeaturesCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ proteinFeaturesCsv: {description: "A CSV file containing protein feature information, must be in the same directory as `geneDataCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ transExonDataCsv: {description: "A CSV file containing transcript exon information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transSpliceDataCsv`.", category: "required"}
+ transSpliceDataCsv: {description: "A CSV file containing transcript splicing information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transExonDataCsv`.", category: "required"}
+
+
+ threads: {description: "The number of threads the program will use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task Sage {
+ input {
+ String tumorName
+ File tumorBam
+ File tumorBamIndex
+ File referenceFasta
+ File referenceFastaDict
+ File referenceFastaFai
+ File hotspots
+ File panelBed
+ File highConfidenceBed
+ Boolean hg38 = false
+ Boolean panelOnly = false
+ String outputPath = "./sage.vcf.gz"
+
+ String? referenceName
+ File? referenceBam
+ File? referenceBamIndex
+ Int? hotspotMinTumorQual
+ Int? panelMinTumorQual
+ Int? hotspotMaxGermlineVaf
+ Int? hotspotMaxGermlineRelRawBaseQual
+ Int? panelMaxGermlineVaf
+ Int? panelMaxGermlineRelRawBaseQual
+ String? mnvFilterEnabled
+ File? coverageBed
+
+ Int threads = 32
+ String javaXmx = "16G"
+ String memory = "20GiB"
+ Int timeMinutes = 720
+ String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_1"
+ }
+
+ command {
+ SAGE -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -tumor ~{tumorName} \
+ -tumor_bam ~{tumorBam} \
+ ~{"-reference " + referenceName} \
+ ~{"-reference_bam " + referenceBam} \
+ -ref_genome ~{referenceFasta} \
+ -hotspots ~{hotspots} \
+ -panel_bed ~{panelBed} \
+ -high_confidence_bed ~{highConfidenceBed} \
+ -assembly ~{true="hg38" false="hg19" hg38} \
+ ~{"-hotspot_min_tumor_qual " + hotspotMinTumorQual} \
+ ~{"-panel_min_tumor_qual " + panelMinTumorQual} \
+ ~{"-hotspot_max_germline_vaf " + hotspotMaxGermlineVaf} \
+ ~{"-hotspot_max_germline_rel_raw_base_qual " + hotspotMaxGermlineRelRawBaseQual} \
+ ~{"-panel_max_germline_vaf " + panelMaxGermlineVaf} \
+ ~{"-panel_max_germline_rel_raw_base_qual " + panelMaxGermlineRelRawBaseQual} \
+ ~{"-mnv_filter_enabled " + mnvFilterEnabled} \
+ ~{"-coverage_bed " + coverageBed} \
+ ~{true="-panel_only" false="" panelOnly} \
+ -threads ~{threads} \
+ -out ~{outputPath}
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ File? referenceSageBqrPng = "~{referenceName}.sage.bqr.png"
+ File? referenceSageBqrTsv = "~{referenceName}.sage.bqr.tsv"
+ File tumorSageBqrPng = "~{tumorName}.sage.bqr.png"
+ File tumorSageBqrTsv = "~{tumorName}.sage.bqr.tsv"
+ File sageGeneCoverageTsv = "~{tumorName}.sage.gene.coverage.tsv"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ cpu: threads
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ tumorBam: {description: "The BAM file for the tumor sample.", category: "required"}
+ tumorBamIndex: {description: "The index of the BAM file for the tumor sample.", category: "required"}
+ referenceName: {description: "The name of the normal/reference sample.", category: "common"}
+ referenceBam: {description: "The BAM file for the normal sample.", category: "common"}
+ referenceBamIndex: {description: "The index of the BAM file for the normal sample.", category: "common"}
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ hotspots: {description: "A vcf file with hotspot variant sites.", category: "required"}
+ panelBed: {description: "A bed file describing coding regions to search for in frame indels.", category: "required"}
+ highConfidenceBed: {description: "A bed files describing high confidence mapping regions.", category: "required"}
+ hotspotMinTumorQual: {description: "Equivalent to sage's `hotspot_min_tumor_qual` option.", category: "advanced"}
+ panelMinTumorQual: {description: "Equivalent to sage's `panel_min_tumor_qual` option.", category: "advanced"}
+ hotspotMaxGermlineVaf: {description: "Equivalent to sage's `hotspot_max_germline_vaf` option.", category: "advanced"}
+ hotspotMaxGermlineRelRawBaseQual: {description: "Equivalent to sage's `hotspot_max_germline_rel_raw_base_qual` option.", category: "advanced"}
+ panelMaxGermlineVaf: {description: "Equivalent to sage's `panel_max_germline_vaf` option.", category: "advanced"}
+ panelMaxGermlineRelRawBaseQual: {description: "Equivalent to sage's `panel_max_germline_vaf` option.", category: "advanced"}
+ mnvFilterEnabled: {description: "Equivalent to sage's `mnv_filter_enabled` option.", category: "advanced"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
+task VirusInterpreter {
+ input {
+ String sampleId
+ File purplePurityTsv
+ File prupleQcFile
+ File tumorSampleWgsMetricsFile
+ File virusBreakendTsv
+ File taxonomyDbTsv
+ File virusReportingDbTsv
+ String outputDir = "."
+
+ String memory = "3GiB"
+ String javaXmx = "2G"
+ Int timeMinutes = 15
+ String dockerImage = "quay.io/biowdl/virus-interpreter:1.2"
+ }
+
+ command {
+ virus-interpreter -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -sample_id ~{sampleId} \
+ -purple_purity_tsv ~{purplePurityTsv} \
+ -purple_qc_file ~{prupleQcFile} \
+ -tumor_sample_wgs_metrics_file ~{tumorSampleWgsMetricsFile} \
+ -virus_breakend_tsv ~{virusBreakendTsv} \
+ -taxonomy_db_tsv ~{taxonomyDbTsv} \
+ -virus_reporting_db_tsv ~{virusReportingDbTsv} \
+ -output_dir ~{outputDir}
+ }
+
+ output {
+ File virusAnnotatedTsv = "~{outputDir}/~{sampleId}.virus.annotated.tsv"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ sampleId: {description: "The name of the sample.", category: "required"}
+ purplePurityTsv: {description: "The purity file produced by purple.", category: "required"}
+ prupleQcFile: {description: "The QC file produced by purple.", category: "required"}
+ tumorSampleWgsMetricsFile: {description: "The picard WGS metrics file for this sample.", category: "required"}
+ virusBreakendTsv: {description: "The TSV output from virusbreakend.", category: "required"}
+ taxonomyDbTsv: {description: "A taxonomy database tsv.", category: "required"}
+ virusReportingDbTsv: {description: "A virus reporting tsv.", category: "required"}
+ outputDir: {description: "The directory the output will be written to.", category: "required"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
diff --git a/htseq.wdl b/htseq.wdl
index cbd8e2ac..92bc4423 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -27,13 +27,14 @@ task HTSeqCount {
String outputTable = "output.tsv"
String order = "pos"
String stranded = "no"
+ Array[String] additionalAttributes = []
+
String? featureType
String? idattr
- Array[String] additionalAttributes = []
Int nprocesses = 1
- String memory = "8G"
- Int timeMinutes = 10 + ceil(size(inputBams, "G") * 60)
+ String memory = "8GiB"
+ Int timeMinutes = 1440 #10 + ceil(size(inputBams, "GiB") * 60) FIXME
String dockerImage = "quay.io/biocontainers/htseq:0.12.4--py37hb3f55d8_0"
}
@@ -58,24 +59,27 @@ task HTSeqCount {
runtime {
cpu: nprocesses
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
+ # inputs
inputBams: {description: "The input BAM files.", category: "required"}
gtfFile: {description: "A GTF/GFF file containing the features of interest.", category: "required"}
outputTable: {description: "The path to which the output table should be written.", category: "common"}
- nprocesses: {description: "Number of processes to run htseq with.", category: "advanced"}
order: {description: "Equivalent to the -r option of htseq-count.", category: "advanced"}
stranded: {description: "Equivalent to the -s option of htseq-count.", category: "common"}
+ additionalAttributes: {description: "Equivalent to the --additional-attr option of htseq-count.", category: "advanced"}
featureType: {description: "Equivalent to the --type option of htseq-count.", category: "advanced"}
idattr: {description: "Equivalent to the --idattr option of htseq-count.", category: "advanced"}
- additionalAttributes: {description: "Equivalent to the --additional-attr option of htseq-count.", category: "advanced"}
+ nprocesses: {description: "Number of processes to run htseq with.", category: "advanced"}
memory: {description: "The amount of memory the job requires in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ counts: {description: "Count table based on input BAM file."}
}
}
diff --git a/isoseq3.wdl b/isoseq3.wdl
index 604a71d5..77f19f80 100644
--- a/isoseq3.wdl
+++ b/isoseq3.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2020 Sequencing Analysis Support Core - Leiden University Medical Center
+# Copyright (c) 2020 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -26,14 +26,15 @@ task Refine {
Boolean requirePolyA = false
String logLevel = "WARN"
File inputBamFile
+ File inputBamIndex
File primerFile
String outputDir
String outputNamePrefix
- Int cores = 2
- String memory = "2G"
+ Int threads = 2
+ String memory = "2GiB"
Int timeMinutes = 30
- String dockerImage = "quay.io/biocontainers/isoseq3:3.3.0--0"
+ String dockerImage = "quay.io/biocontainers/isoseq3:3.4.0--0"
}
command {
@@ -43,7 +44,7 @@ task Refine {
--min-polya-length ~{minPolyALength} \
~{true="--require-polya" false="" requirePolyA} \
--log-level ~{logLevel} \
- --num-threads ~{cores} \
+ --num-threads ~{threads} \
--log-file "~{outputDir}/~{outputNamePrefix}.stderr.log" \
~{inputBamFile} \
~{primerFile} \
@@ -60,7 +61,7 @@ task Refine {
}
runtime {
- cpu: cores
+ cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
@@ -72,10 +73,11 @@ task Refine {
requirePolyA: {description: "Require fl reads to have a poly(A) tail and remove it.", category: "common"}
logLevel: {description: "Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).", category: "advanced"}
inputBamFile: {description: "Bam input file.", category: "required"}
+ inputBamIndex: {description: "Index for the Bam input file.", category: "required"}
primerFile: {description: "Barcode/primer fasta file.", category: "required"}
outputDir: {description: "Output directory path.", category: "required"}
outputNamePrefix: {description: "Basename of the output files.", category: "required"}
- cores: {description: "The number of cores to be used.", category: "advanced"}
+ threads: {description: "The number of threads to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
diff --git a/lima.wdl b/lima.wdl
index 2e8a7085..eece2b3f 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2020 Sequencing Analysis Support Core - Leiden University Medical Center
+# Copyright (c) 2020 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -48,15 +48,15 @@ task Lima {
File barcodeFile
String outputPrefix
- Int cores = 2
- String memory = "2G"
+ Int threads = 2
+ String memory = "2GiB"
Int timeMinutes = 30
- String dockerImage = "quay.io/biocontainers/lima:1.11.0--0"
+ String dockerImage = "quay.io/biocontainers/lima:2.2.0--h9ee0642_0"
}
Map[String, String] libraryDesignOptions = {"same": "--same", "different": "--different", "neighbors": "--neighbors"}
- command {
+ command <<<
set -e
mkdir -p "$(dirname ~{outputPrefix})"
lima \
@@ -82,34 +82,31 @@ task Lima {
--guess-min-count ~{guessMinCount} \
~{true="--peek-guess" false="" peekGuess} \
--log-level ~{logLevel} \
- --num-threads ~{cores} \
- ~{"--log-file " + outputPrefix + ".fl.stderr.log"} \
+ --num-threads ~{threads} \
+ ~{"--log-file " + outputPrefix + ".lima.stderr.log"} \
~{inputBamFile} \
~{barcodeFile} \
- ~{basename(outputPrefix) + ".fl.bam"}
+ ~{outputPrefix + ".bam"}
- # copy commands below are needed because glob command does not find
- # multiple bam/bam.pbi/subreadset.xml files when not located in working
- # directory.
- cp "~{basename(outputPrefix)}.fl.json" "~{outputPrefix}.fl.json"
- cp "~{basename(outputPrefix)}.fl.lima.counts" "~{outputPrefix}.fl.lima.counts"
- cp "~{basename(outputPrefix)}.fl.lima.report" "~{outputPrefix}.fl.lima.report"
- cp "~{basename(outputPrefix)}.fl.lima.summary" "~{outputPrefix}.fl.lima.summary"
- }
+ dirName="$(dirname ~{outputPrefix})"
+ find "$(cd ${dirName}; pwd)" -name "*.bam" > bamFiles.txt
+ find "$(cd ${dirName}; pwd)" -name "*.bam.pbi" > bamIndexes.txt
+ find "$(cd ${dirName}; pwd)" -name "*.consensusreadset.xml" > consensusreadset.txt
+ >>>
output {
- Array[File] limaBam = glob("*.bam")
- Array[File] limaBamIndex = glob("*.bam.pbi")
- Array[File] limaXml = glob("*.subreadset.xml")
- File limaStderr = outputPrefix + ".fl.stderr.log"
- File limaJson = outputPrefix + ".fl.json"
- File limaCounts = outputPrefix + ".fl.lima.counts"
- File limaReport = outputPrefix + ".fl.lima.report"
- File limaSummary = outputPrefix + ".fl.lima.summary"
+ Array[File] limaBam = read_lines("bamFiles.txt")
+ Array[File] limaBamIndex = read_lines("bamIndexes.txt")
+ Array[File] limaXml = read_lines("consensusreadset.txt")
+ File limaStderr = outputPrefix + ".lima.stderr.log"
+ File limaJson = outputPrefix + ".json"
+ File limaCounts = outputPrefix + ".lima.counts"
+ File limaReport = outputPrefix + ".lima.report"
+ File limaSummary = outputPrefix + ".lima.summary"
}
runtime {
- cpu: cores
+ cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
@@ -142,7 +139,7 @@ task Lima {
inputBamFile: {description: "Bam input file.", category: "required"}
barcodeFile: {description: "Barcode/primer fasta file.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
- cores: {description: "The number of cores to be used.", category: "advanced"}
+ threads: {description: "The number of threads to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
diff --git a/macs2.wdl b/macs2.wdl
index fad3cb00..5ccc5a5f 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -24,14 +24,21 @@ task PeakCalling {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
- Array[File]+? controlBams
- Array[File]+? controlBamsIndex
- String outDir
+ Array[File] controlBams
+ Array[File] controlBamsIndex
+ String outDir = "macs2"
String sampleName
+ String format = "AUTO"
Boolean nomodel = false
-
- Int threads = 1
- String memory = "8G"
+ String? gensz
+ Int? extsize
+ Int? shiftsize
+ Float? pval_thres
+ Boolean bdg = false
+ String? keepdup
+ Boolean callsummits = false
+ Int timeMinutes = 600 # Default to 10 hours
+ String memory = "8GiB"
String dockerImage = "quay.io/biocontainers/macs2:2.1.2--py27r351_0"
}
@@ -39,10 +46,18 @@ task PeakCalling {
set -e
macs2 callpeak \
--treatment ~{sep = ' ' inputBams} \
- ~{true="--control" false="" defined(controlBams)} ~{sep = ' ' controlBams} \
+ ~{true="--control" false="" length(controlBams) > 0} ~{sep = ' ' controlBams} \
--outdir ~{outDir} \
--name ~{sampleName} \
- ~{true='--nomodel' false='' nomodel}
+ ~{"-f " + format} \
+ ~{"-g " + gensz} \
+ ~{"-p " + pval_thres} \
+ ~{"--shift " + shiftsize} \
+ ~{"--extsize " + extsize} \
+ ~{true='--nomodel' false='' nomodel} \
+ ~{true='-B' false='' bdg} \
+ ~{"--keep-dup " + keepdup} \
+ ~{true='--call-summits' false='' callsummits}
}
output {
@@ -50,8 +65,29 @@ task PeakCalling {
}
runtime {
- cpu: threads
+ cpu: 1
memory: memory
docker: dockerImage
+ time_minutes: timeMinutes
+ }
+ parameter_meta {
+ inputBams: {description: "The BAM files on which to perform peak calling.", category: "required"}
+ inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
+ controlBams: {description: "Control BAM files for the input bam files.", category: "common"}
+ controlBamsIndex: {description: "The indexes for the control BAM files.", category: "common"}
+ sampleName: {description: "Name of the sample to be analysed", category: "required"}
+ outDir: {description: "All output files will be written in this directory.", category: "advanced"}
+ nomodel: {description: "Whether or not to build the shifting model.", category: "advanced"}
+ gensz: {description: "macs2 argument for setting the mappable genome size or effective genome size which is defined as the genome size which can be sequenced.", category: "advanced"}
+ pval_thres: {description: "macs2 argument for setting the p-value cutoff. If -p is specified, MACS2 will use p-value instead of q-value.", category: "advanced"}
+ shiftsize: {description: "macs2 argument to set an arbitrary shift in bp. Can be negative to indicate direction.", category: "advanced"}
+ extsize: {description: "macs2 argument to extend reads in 5'->3' direction to fix-sized fragments.", category: "advanced"}
+ bdg: {description: "macs2 argument that enables the storage of the fragment pileup, control lambda in bedGraph files.", category: "advanced"}
+ keepdup: {description: "macs2 argument that controls the behavior towards duplicate tags at the exact same location.", category: "advanced"}
+ callsummits: {description: "macs2 argument to reanalyze the shape of signal profile to deconvolve subpeaks within each peak called from the general procedure.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ format: {description: "Which format to use. Use BAMPE for paired-end reads.", category: "common"}
}
-}
\ No newline at end of file
+}
diff --git a/manta.wdl b/manta.wdl
index 5382d2a5..fde8c208 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -27,13 +27,14 @@ task Germline {
File referenceFasta
File referenceFastaFai
String runDir = "./manta_run"
+ Boolean exome = false
+
File? callRegions
File? callRegionsIndex
- Boolean exome = false
Int cores = 1
Int memoryGb = 4
- Int timeMinutes = 60
+ Int timeMinutes = 2880
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
@@ -59,7 +60,7 @@ task Germline {
runtime {
cpu: cores
- memory: "~{memoryGb}G"
+ memory: "~{memoryGb}GiB"
docker: dockerImage
time_minutes: timeMinutes
}
@@ -71,13 +72,17 @@ task Germline {
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
runDir: {description: "The directory to use as run/output directory.", category: "common"}
+ exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
- exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
cores: {description: "The the number of cores required to run a program", category: "required"}
memoryGb: {description: "The memory required to run the manta", category: "required"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ mantaVCF: {description: "SVs and indels scored and genotyped under a diploid model for the set of samples in a joint diploid sample analysis or for the normal sample in a tumor/normal subtraction analysis."}
+ mantaVCFindex: {description: "Index of output mantaVCF."}
}
}
@@ -85,18 +90,19 @@ task Somatic {
input {
File tumorBam
File tumorBamIndex
- File? normalBam
- File? normalBamIndex
File referenceFasta
File referenceFastaFai
String runDir = "./manta_run"
+ Boolean exome = false
+
+ File? normalBam
+ File? normalBamIndex
File? callRegions
File? callRegionsIndex
- Boolean exome = false
Int cores = 1
Int memoryGb = 4
- Int timeMinutes = 60
+ Int timeMinutes = 2880
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
@@ -132,25 +138,36 @@ task Somatic {
runtime {
cpu: cores
- memory: "~{memoryGb}G"
+ memory: "~{memoryGb}GiB"
docker: dockerImage
time_minutes: timeMinutes
}
parameter_meta {
+ # inputs
tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
- normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
- normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "common"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
runDir: {description: "The directory to use as run/output directory.", category: "common"}
+ exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
+ normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
+ normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "common"}
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
- exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ candidateSmallIndelsVcf: {description: "Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion variants less than the minimum scored variant size."}
+ candidateSmallIndelsVcfIndex: {description: "Index of output VCF file candidateSmallIndelsVcf."}
+ candidateSVVcf: {description: "Unscored SV and indel candidates."}
+ candidatSVVcfIndex: {description: "Index of output VCF file candidateSVVcf."}
+ tumorSVVcf: {description: "Subset of the candidateSV.vcf.gz file after removing redundant candidates and small indels less than the minimum scored variant size."}
+ tumorSVVcfIndex: {description: "Index of output VCF file tumorSVVcf."}
+ diploidSV: {description: "SVs and indels scored and genotyped under a diploid model for the set of samples in a joint diploid sample analysis or for the normal sample in a tumor/normal subtraction analysis."}
+ diploidSVindex: {description: "Index of output VCF file diploidSV."}
}
}
diff --git a/minimap2.wdl b/minimap2.wdl
index fb31fb7f..a7584beb 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+# Copyright (c) 2019 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -31,9 +31,9 @@ task Indexing {
Int? splitIndex
Int cores = 1
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 10
- String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+ String dockerImage = "quay.io/biocontainers/minimap2:2.20--h5bf99c6_0"
}
command {
@@ -61,7 +61,7 @@ task Indexing {
}
parameter_meta {
- # input
+ # inputs
useHomopolymerCompressedKmer: {description: "Use homopolymer-compressed k-mer (preferrable for pacbio).", category: "advanced"}
kmerSize: {description: "K-mer size (no larger than 28).", category: "advanced"}
minimizerWindowSize: {description: "Minimizer window size.", category: "advanced"}
@@ -73,7 +73,7 @@ task Indexing {
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
- # output
+ # outputs
indexFile: {description: "Indexed reference file."}
}
}
@@ -81,52 +81,82 @@ task Indexing {
task Mapping {
input {
String presetOption
- Int kmerSize = 15
- Boolean skipSelfAndDualMappings = false
- Boolean outputSam = false
String outputPrefix
- Boolean addMDTagToSam = false
- Boolean secondaryAlignment = false
File referenceFile
File queryFile
+
+ Int compressionLevel = 1
+ Boolean nameSorted = false
+ # MM, ML, MN -> Methylation flags
+ # Also keep the following flags for Sequali to be able to run on the mapped bam file and get ONT information.
+ # ch -> channel
+ # st -> start time
+ # du -> duration
+ # dx -> Whether read was duplex
+ # pi -> Parent ID for split read
+
+ String tagsToKeep = "MM,ML,MN,ch,st,du,dx,pi"
+ Boolean skipSelfAndDualMappings = false
+ Boolean addMDTagToSam = false
+ Boolean secondaryAlignment = true
+
+ Int? kmerSize
Int? maxIntronLength
Int? maxFragmentLength
Int? retainMaxSecondaryAlignments
Int? matchingScore
Int? mismatchPenalty
String? howToFindGTAG
+ String? readgroup
- Int cores = 4
- String memory = "30G"
+ Int sortThreads = 2
+ Int sortMemoryGb = 1
+ Int cores = 8
+ String memory = "24GiB"
Int timeMinutes = 1 + ceil(size(queryFile, "G") * 200 / cores)
- String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+ # Minimap 2.28 samtools 1.20
+ String dockerImage = "quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
}
- command {
- set -e
+ # Always run data through samtools fastq. This supports both FASTQ and uBAM
+ # files. It does remove any existing FASTQ comments, but this should not be
+ # problematic for most files.
+
+ command <<<
+ set -e -o pipefail
mkdir -p "$(dirname ~{outputPrefix})"
+ samtools fastq -T "~{tagsToKeep}" ~{queryFile} | \
minimap2 \
+ -a \
-x ~{presetOption} \
- -k ~{kmerSize} \
~{true="-X" false="" skipSelfAndDualMappings} \
- ~{true="-a" false="" outputSam} \
- -o ~{outputPrefix} \
~{true="--MD" false="" addMDTagToSam} \
--secondary=~{true="yes" false="no" secondaryAlignment} \
+ -y \
-t ~{cores} \
+ ~{"-k " + kmerSize} \
~{"-G " + maxIntronLength} \
~{"-F " + maxFragmentLength} \
~{"-N " + retainMaxSecondaryAlignments} \
~{"-A " + matchingScore} \
~{"-B " + mismatchPenalty} \
~{"-u " + howToFindGTAG} \
+ ~{"-R '" + readgroup}~{false="" true="'" defined(readgroup)} \
~{referenceFile} \
- ~{queryFile}
- }
+ - \
+ | samtools sort \
+ ~{true="-N" false="" nameSorted} \
+ --threads ~{sortThreads - 1} \
+ -l ~{compressionLevel} \
+ -m ~{sortMemoryGb}G \
+ -o ~{outputPrefix}.bam
+ samtools index ~{outputPrefix}.bam
+ >>>
output {
- File alignmentFile = outputPrefix
+ File bam = "~{outputPrefix}.bam"
+ File bamIndex = "~{outputPrefix}.bam.bai"
}
runtime {
@@ -137,27 +167,34 @@ task Mapping {
}
parameter_meta {
+ # inputs
presetOption: {description: "This option applies multiple options at the same time.", category: "common"}
kmerSize: {description: "K-mer size (no larger than 28).", category: "advanced"}
- outputSam: {description: "Output in the sam format.", category: "common"}
+ skipSelfAndDualMappings: {description: "Skip self and dual mappings (for the all-vs-all mode).", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ addMDTagToSam: {description: "Adds a MD tag to the sam output file.", category: "common"}
+ secondaryAlignment: {description: "Whether to output secondary alignments.", category: "advanced"}
+ referenceFile: {description: "Reference fasta file.", category: "required"}
+ queryFile: {description: "Input fasta file.", category: "required"}
maxIntronLength: {description: "Max intron length (effective with -xsplice; changing -r).", category: "advanced"}
maxFragmentLength: {description: "Max fragment length (effective with -xsr or in the fragment mode).", category: "advanced"}
- skipSelfAndDualMappings: {description: "Skip self and dual mappings (for the all-vs-all mode).", category: "advanced"}
retainMaxSecondaryAlignments: {description: "Retain at most N secondary alignments.", category: "advanced"}
matchingScore: {description: "Matching score.", category: "advanced"}
mismatchPenalty: {description: "Mismatch penalty.", category: "advanced"}
+ tagsToKeep: {description: "Tags to keep from the input unaligned BAM file.", category: "Advanced"}
howToFindGTAG: {description: "How to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG.", category: "common"}
- addMDTagToSam: {description: "Adds a MD tag to the sam output file.", category: "common"}
- secondaryAlignment: {description: "Whether to output secondary alignments.", category: "advanced"}
- referenceFile: {description: "Reference fasta file.", category: "required"}
- queryFile: {description: "Input fasta file.", category: "required"}
+ compressionLevel: {description: "compressionLevel for the output file", category: "advanced"}
+ sortThreads: {description: "Extra sorting threads used for samtools sort", category: "advanced"}
+ sortMemoryGb: {description: "Amount of memory set for sorting", category: "advanced"}
+ nameSorted: {description: "Output a name sorted file instead", category: "common"}
+
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
- # output
- alignmentFile: {description: "Mapping and alignment between collections of dna sequences file."}
+ # outputs
+ bam: {description: "Mapping and alignment between collections of dna sequences file in BAM format."}
+ bamIndex: {description: "Accompanying index file for the BAM file."}
}
}
diff --git a/modkit.wdl b/modkit.wdl
new file mode 100644
index 00000000..ddf4dbf7
--- /dev/null
+++ b/modkit.wdl
@@ -0,0 +1,250 @@
+version 1.0
+
+# Copyright (c) 2025 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Pileup {
+ input {
+ File bam
+ File bamIndex
+ String outputBed = "output.bedMethyl"
+ String outputBedGraph = "combined.bedgraph"
+ File referenceFasta
+ File referenceFastaFai
+
+ Int? intervalSize
+ File? includeBed
+ String? filterThreshold
+ String? filterPercentile
+
+ Boolean cpg = false
+ Boolean combineMods = false
+ Boolean combineStrands = false
+ String? ignore
+ String logFilePath = "modkit.log"
+
+ Int threads = 8
+ String memory = "4GiB"
+ Int timeMinutes = 2880 / threads # 2 Days / threads
+ String dockerImage = "quay.io/biocontainers/ont-modkit:0.4.3--hcdda2d0_0"
+ }
+
+ command <<<
+ set -e
+ mkdir -p $(dirname ~{outputBed})
+ mkdir -p $(dirname ~{logFilePath})
+ modkit pileup \
+ --threads ~{threads} \
+ ~{"--interval-size " + intervalSize} \
+ ~{"--include-bed " + includeBed} \
+ ~{"--ignore " + ignore} \
+ --ref ~{referenceFasta} \
+ ~{true="--cpg" false="" cpg} \
+ ~{true="--combine-mods" false="" combineMods} \
+ ~{true="--combine-strands" false="" combineStrands} \
+ ~{"--filter-percentile " + filterPercentile} \
+ ~{"--filter-threshold " + filterThreshold} \
+ --log-filepath ~{logFilePath} \
+ ~{bam} \
+ - | tee ~{outputBed} | awk -v OFS="\t" '{print $1, $2, $3, $11, $10 >> "~{outputBedGraph}_"$4"_"$6".bedGraph"}'
+ # Separately generate the combined file as well, so users can have a choice.
+ cat ~{outputBed} | awk -v OFS="\t" '{print $1, $2, $3, $11, $10}' > ~{outputBedGraph}
+ >>>
+
+ # You can use modkit pileup ${bam_path} - | tee out.bedmethyl | awk -v OFS="\t" '{print $1, $2, $3, $11, $10}' > out.bg to get both outputs at once without running anything twice.
+ # https://github.com/nanoporetech/modkit/issues/210#issuecomment-2181706374
+
+ output {
+ File out = outputBed # Normal mode
+ File outGraph = outputBedGraph # Normal mode
+ Array[File] outFiles = glob(outputBedGraph + "*.bedGraph") # Bedgraph mode
+ File logFile = logFilePath
+ }
+
+ runtime {
+ docker: dockerImage
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes
+ }
+
+ parameter_meta {
+ # input
+ bam: {description: "The input alignment file", category: "required"}
+ bamIndex: {description: "The index for the input alignment file", category: "required"}
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ outputBed: {description: "The output name where the bedMethyl file should be placed.", category: "common"}
+ outputBedGraph: {description: "The output name where the bedgraph file should be placed", category: "common"}
+
+ intervalSize: {description: "Sets the interval size", category: "advanced"}
+ includeBed: {description: "Bed file with regions to include", category: "advanced"}
+ cpg: {description: "Whether to call only at cpg sites", category: "advanced"}
+ combineMods: {description: "Whether to combine modifications in the output", category: "advanced"}
+ combineStrands: {description: "Whether to combine strands in the output", category: "advanced"}
+ ignore: {description: "Modification type to ignore. For example 'h'.", category: "advanced"}
+ logFilePath: {description: "Path where the log file should be written.", category: "advanced"}
+ filterThreshold: {description: "Global filter threshold can be specified with by a decimal number (e.g. 0.75). Otherwise the automatic filter percentile will be used.", category: "advanced"}
+ filterPercentile: {description: "This defaults to 0.1, to remove the lowest 10% confidence modification calls, but can be manually adjusted", category: "advanced"}
+
+ threads: {description: "The number of threads to use for variant calling.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # output
+ out: {description: "The output bed files. Not available when bedgraph = true."}
+ outFiles: {description: "Output files when bedgraph = true."}
+ logFile: {description: "The generated log file."}
+ }
+}
+
+task Summary {
+ input {
+ File bam
+ File bamIndex
+
+ String summary = "modkit.summary.txt"
+
+ Boolean sample = true
+ Int? numReads # = 10042
+ Float? samplingFrac # = 0.1
+ Int? seed
+
+ Int threads = 4
+ String memory = ceil(size(bam, "GiB") * 0.1) + 5 # Based on a linear model with some fudge (memory = 0.07540 * file_size - 0.6).
+ Int timeMinutes = 60 # originally this was set at "2 Days / threads" but with 4 threads and that much ram, it's pretty fast.
+ String dockerImage = "quay.io/biocontainers/ont-modkit:0.4.3--hcdda2d0_0"
+ }
+
+ command <<<
+ set -e
+ mkdir -p $(dirname ~{summary})
+
+ modkit summary \
+ --threads ~{threads} \
+ ~{true="" false="--no-sampling" sample} \
+ ~{"--num-reads " + numReads} \
+ ~{"--sampling-frac " + samplingFrac} \
+ ~{"--seed " + seed} \
+ ~{bam} > ~{summary}
+ >>>
+
+ output {
+ File summaryReport = summary # Normal mode
+ }
+
+ runtime {
+ docker: dockerImage
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes
+ }
+
+ parameter_meta {
+ # input
+ bam: {description: "The input alignment file", category: "required"}
+ bamIndex: {description: "The index for the input alignment file", category: "required"}
+
+ sample: {description: "Allows you to disable sampling and report stats for the whole file.", category: "advanced"}
+ numReads: {description: "By default a fixed amount of reads are read, you can set this to change the number of reads to sample.", category: "advanced"}
+ samplingFrac: {description: "Use a fixed percentage of reads, rather than a fixed number of reads, for sampling.", category: "advanced"}
+ seed: {description: "A seed can be provided for reproducibility in the sampling fraction case.", category: "advanced"}
+
+ threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # output
+ summaryReport: {description: "The output modkit summary."}
+ }
+}
+
+task SampleProbs {
+ input {
+ File bam
+ File bamIndex
+
+ String summary = "modkit-sample-probs"
+
+ Boolean sample = true
+ Int? numReads # = 10042
+ Float? samplingFrac # = 0.1
+ Int? seed
+
+ Int threads = 4
+ String memory = "32G"
+ Int timeMinutes = 60
+ String dockerImage = "quay.io/biocontainers/ont-modkit:0.4.3--hcdda2d0_0"
+ }
+
+ command <<<
+ set -e
+ mkdir -p ~{summary}
+
+ modkit sample-probs \
+ --threads ~{threads} \
+ --out-dir ~{summary} \
+ ~{true="" false="--no-sampling" sample} \
+ ~{"--num-reads " + numReads} \
+ ~{"--sampling-frac " + samplingFrac} \
+ ~{"--seed " + seed} \
+ --hist \
+ ~{bam}
+ >>>
+
+ output {
+ File reportCounts = "~{summary}/counts.html"
+ File reportProportion = "~{summary}/proportion.html"
+ File reportProbabilitiesTsv = "~{summary}/probabilities.tsv"
+ File reportThresholdsTsv = "~{summary}/thresholds.tsv"
+ }
+
+ runtime {
+ docker: dockerImage
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes
+ }
+
+ parameter_meta {
+ # input
+ bam: {description: "The input alignment file", category: "required"}
+ bamIndex: {description: "The index for the input alignment file", category: "required"}
+ summary: {description: "A folder for the outputs", category: "required"}
+
+ sample: {description: "Allows you to disable sampling and report stats for the whole file.", category: "advanced"}
+ numReads: {description: "By default a fixed amount of reads are read, you can set this to change the number of reads to sample.", category: "advanced"}
+ samplingFrac: {description: "Use a fixed percentage of reads, rather than a fixed number of reads, for sampling.", category: "advanced"}
+ seed: {description: "A seed can be provided for reproducibility in the sampling fraction case.", category: "advanced"}
+
+ threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # output
+ reportCounts: {description: "The output html report of counts"}
+ reportProportion: {description: "The output html report of proportions"}
+ reportProbabilitiesTsv: {description: "The output TSV of Probabilities"}
+ reportThresholdsTsv: {description: "The output TSV of thresholds"}
+ }
+}
diff --git a/mosdepth.wdl b/mosdepth.wdl
new file mode 100644
index 00000000..43e95614
--- /dev/null
+++ b/mosdepth.wdl
@@ -0,0 +1,106 @@
+version 1.0
+
+# Copyright (c) 2025 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Mosdepth {
+ input {
+ File bam
+ File bamIndex
+ String prefix = "./out"
+
+ String? chrom
+ # --by flag takes a BED file or an integer. So there need to be two inputs in WDL's typed system.
+ File? byBed
+ Int? byWindow
+ File? fasta
+ Int? flag
+ Int? includeFlag
+
+ Boolean noPerBase = false
+ Boolean d4 = false
+ Boolean fastMode = false
+
+ Int threads = 1
+ String memory = "4GiB"
+ Int timeMinutes = 10 + ceil(size(bam, "G")) * 4
+ String dockerImage = "quay.io/biocontainers/mosdepth:0.3.10--h4e814b3_1"
+ }
+
+ command <<<
+ set -e
+ mkdir -p $(dirname ~{prefix})
+ mosdepth \
+ --threads ~{threads} \
+ ~{"--chrom " + chrom} \
+ ~{"--by " + byBed} \
+ ~{"--by " + byWindow} \
+ ~{"--fasta " + fasta} \
+ ~{true="--no-per-base" false="" noPerBase} \
+ ~{true="--d4" false="" d4} \
+ ~{"--flag " + flag} \
+ ~{"--include-flag " + includeFlag} \
+ ~{true="--fast-mode" false="" fastMode} \
+ ~{prefix} ~{bam}
+ >>>
+
+ output {
+ File globalDist = "~{prefix}.mosdepth.global.dist.txt"
+ File summary = "~{prefix}.mosdepth.summary.txt"
+ File? perBaseBed = "~{prefix}.per-base.bed.gz"
+ File? regionsBed = "~{prefix}.regions.bed.gz"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ bam: {description: "Input BAM or CRAM file.", category: "required"}
+ bamIndex: {description: "Index for the input BAM or CRAM file.", category: "required"}
+ prefix: {description: "Output prefix.", category: "common"}
+
+ chrom: {description: "Chromosome to restrict depth calculation.", category: "advanced"}
+ byBed: {description: "Bed file with windows to include for the --by flag. Should not be used together with byWindow.", category: "common"}
+ byWindow: {description: "Integer window size for the --by flag. Should not be used together with byBed.", category: "advanced"}
+ fasta: {description: "FASTA file, only necessary when CRAM input is used.", category: "advanced"}
+ flag: {description: "Exclude reads with any of the bits in FLAG set.", category: "advanced"}
+ includeFlag: {description: "Only include reads with any of the bits in FLAG set.", category: "advanced"}
+
+ noPerBase: {description: "Don't output per-base depth. Skipping this output will speed execution.", category: "common"}
+ d4: {description: "output per-base depth in d4 format.", category: "advanced"}
+ fastMode: {description: "Don't look at internal cigar operations or correct mate overlaps (recommended for most use-cases).", category: "common"}
+
+ threads: {description: "How many threads to use.", category: "common"}
+ memory: {description: "How much memory to allocate.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ globalDist: {description: "Global distribution table file."}
+ summary: {description: "Summary table file."}
+ perBaseBed: {description: "Per base coverage BED file."}
+ regionsBed: {description: "Per region BED file, if byBed or byWindow is used."}
+ }
+}
\ No newline at end of file
diff --git a/multiqc.wdl b/multiqc.wdl
index 7dcf333e..db47ac87 100644
--- a/multiqc.wdl
+++ b/multiqc.wdl
@@ -22,16 +22,29 @@ version 1.0
task MultiQC {
input {
- # Use a string here so cromwell does not relocate an entire analysis directory
+ # Use a string here so cromwell does not relocate an entire
+ # analysis directory.
Array[File] reports
Boolean force = false
Boolean dirs = false
- Int? dirsDepth
Boolean fullNames = false
+ String outDir = "."
+ Boolean dataDir = false
+ Boolean zipDataDir = true
+ Boolean export = false
+ Boolean flat = false
+ Boolean interactive = true
+ Boolean lint = false
+ Boolean pdf = false
+ # This must be actively enabled in my opinion.
+ # The tools default is to upload.
+ Boolean megaQCUpload = false
+ Boolean enableAi = false
+
+ Int? dirsDepth
String? title
String? comment
String? fileName
- String outDir = "."
String? template
String? tag
String? ignore
@@ -40,22 +53,17 @@ task MultiQC {
File? fileList
Array[String]+? exclude
Array[String]+? module
- Boolean dataDir = false
+ Array[File]+? additionalReports
String? dataFormat
- Boolean zipDataDir = true
- Boolean export = false
- Boolean flat = false
- Boolean interactive = true
- Boolean lint = false
- Boolean pdf = false
- Boolean megaQCUpload = false # This must be actively enabled in my opinion. The tools default is to upload.
File? config # A directory
String? clConfig
+
String? memory
- Int timeMinutes = 2 + ceil(size(reports, "G") * 8)
- String dockerImage = "quay.io/biocontainers/multiqc:1.7--py_1"
+ Int timeMinutes = 10 + ceil(size(reports, "GiB") * 8)
+ String dockerImage = "quay.io/biocontainers/multiqc:1.28--pyhdfd78af_0"
}
- Int memoryGb = 2 + ceil(size(reports, "G"))
+
+ Int memoryGb = 2 + ceil(size(reports, "GiB"))
# This is where the reports end up. It does not need to be changed by the
# user. It is full of symbolic links, so it is not of any use to the user
@@ -69,15 +77,18 @@ task MultiQC {
# By hashing the parent path we make sure there are no file colissions as
# files from the same directory end up in the same directory, while files
# from other directories get their own directory. Cromwell also uses this
- # strategy. Using python's builtin hash is unique enough for these purposes.
-
+ # strategy. Using python's builtin hash is unique enough
+ # for these purposes.
+
+ Array[File] allReports = flatten([reports, flatten(select_all([additionalReports]))])
+
command {
python3 < ~{ntFilePath}
@@ -132,15 +132,16 @@ task DownloadAccessionToTaxId {
command {
set -e -o pipefail
mkdir -p ~{downloadDir}
- rsync -av \
- --partial \
- rsync://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_*.accession2taxid.gz* \
- ~{downloadDir}
+ rsync \
+ -av \
+ --partial \
+ rsync://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_*.accession2taxid.gz* \
+ ~{downloadDir}
(cd ~{downloadDir} && md5sum -c *.md5)
for file in ~{downloadDir}/nucl_*.accession2taxid.gz
do
zcat $file | tail -n +2 | cut -f 2,3 ~{true="| gzip" false='' gzip} > \
- $file.seqtaxmap~{true='.gz' false='' gzip}
+ $file.seqtaxmap~{true='.gz' false='' gzip}
done
}
diff --git a/pacbio.wdl b/pacbio.wdl
new file mode 100644
index 00000000..dcf0f69e
--- /dev/null
+++ b/pacbio.wdl
@@ -0,0 +1,95 @@
+version 1.0
+
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task mergePacBio {
+ input {
+ Array[File]+ reports
+ String outputPathMergedReport
+
+ String memory = "4GiB"
+ String dockerImage = "quay.io/redmar_van_den_berg/pacbio-merge:0.2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPathMergedReport})
+ pacbio_merge \
+ --reports ~{sep=" " reports} \
+ --json-output ~{outputPathMergedReport}
+ }
+
+ runtime {
+ memory: memory
+ docker: dockerImage
+ }
+
+ output {
+ File outputMergedReport = outputPathMergedReport
+ }
+
+ parameter_meta {
+ # inputs
+ reports: {description: "The PacBio report files to merge.", category: "required"}
+ outputPathMergedReport: {description: "The location the merged PacBio report file should be written to.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputMergedReport: {description: "The PacBio reports merged into one."}
+ }
+}
+
+task ccsChunks {
+ input {
+ Int chunkCount
+
+ String memory = "4GiB"
+ String dockerImage = "python:3.7-slim"
+ }
+
+ command {
+ set -e
+ python <7 days and failing.
+ String? read_name_regex
+
+ # In GATK Best practices pipeline MarkDuplicates is given a 7G VM.
# https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L1040
Int javaXmxMb = 6656 # 6.5G
String memoryMb = javaXmxMb + 512
- Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8)
- String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
-
- # The program default for READ_NAME_REGEX is appropriate in nearly every case.
- # Sometimes we wish to supply "null" in order to turn off optical duplicate detection
- # This can be desirable if you don't mind the estimated library size being wrong and
- # optical duplicate detection is taking >7 days and failing
- String? read_name_regex
+ Int timeMinutes = 1 + ceil(size(inputBams, "GiB") * 8)
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
}
# Task is assuming query-sorted input so that the Secondary and Supplementary reads get
# marked correctly. This works because the output of BWA is query-grouped and therefore,
# so is the output of MergeBamAlignment. While query-grouped isn't actually query-sorted,
- # it's good enough for MarkDuplicates with ASSUME_SORT_ORDER="queryname"
-
+ # it's good enough for MarkDuplicates with ASSUME_SORT_ORDER="queryname".
command {
set -e
mkdir -p "$(dirname ~{outputBamPath})"
@@ -501,6 +769,8 @@ task MarkDuplicates {
OUTPUT=~{outputBamPath} \
METRICS_FILE=~{metricsPath} \
COMPRESSION_LEVEL=~{compressionLevel} \
+ USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
+ USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater} \
VALIDATION_STRINGENCY=SILENT \
~{"READ_NAME_REGEX=" + read_name_regex} \
OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 \
@@ -508,8 +778,6 @@ task MarkDuplicates {
CREATE_INDEX=true \
ADD_PG_TAG_TO_READS=false \
CREATE_MD5_FILE=~{true="true" false="false" createMd5File} \
- USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
- USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
}
output {
@@ -520,9 +788,9 @@ task MarkDuplicates {
}
runtime {
- docker: dockerImage
+ memory: "~{memoryMb}MiB"
time_minutes: timeMinutes
- memory: "~{memoryMb}M"
+ docker: dockerImage
}
parameter_meta {
@@ -530,42 +798,49 @@ task MarkDuplicates {
inputBams: {description: "The BAM files for which the duplicate reads should be marked.", category: "required"}
outputBamPath: {description: "The location where the ouptut BAM file should be written.", category: "required"}
metricsPath: {description: "The location where the output metrics file should be written.", category: "required"}
- read_name_regex: {description: "Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.", category: "advanced"}
- createMd5File: {description: "Whether to create a md5 file for the created BAM file.", category: "advanced"}
+ compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
- compressionLevel: {description: "The compression level at which the BAM files are written", category: "advanced"}
+ createMd5File: {description: "Whether to create a md5 file for the created BAM file.", category: "advanced"}
+ read_name_regex: {description: "Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: ""}
+ outputBamIndex: {description: ""}
+ outputBamMd5: {description: ""}
+ metricsFile: {description: ""}
}
}
-# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
+# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs.
task MergeVCFs {
input {
Array[File]+ inputVCFs
Array[File]+ inputVCFsIndexes
String outputVcfPath
-
- String memory = "5G"
- String javaXmx = "4G"
- Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2
- String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
Int compressionLevel = 1
- Boolean useJdkInflater = true # Slightly faster than the intel one.
- # Better results for compression level 1 (much smaller). Higher compression levels similar to intel deflater.
+ Boolean useJdkInflater = false
+ # Better results for compression level 1 (much smaller).
+ # Higher compression levels similar to intel deflater.
# NOTE: this might change in the future when the intel deflater is updated!
- Boolean useJdkDeflater = true
+ # Second NOTE: No it did not change. Only the fastest algorithm with
+ # worse compression is wrapped in the intel GKL. Instead of using
+ # one of the slightly slower but better compressing alternatives from ISA-L.
+ # (Which are also faster than zlib.)
+ Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
+ String javaXmx = "4G"
+ String memory = "5GiB"
+ Int timeMinutes = 1 + ceil(size(inputVCFs, "GiB")) * 2
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
}
- # Using MergeVcfs instead of GatherVcfs so we can create indices
- # See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
-
+ # Using MergeVcfs instead of GatherVcfs so we can create indices.
+ # See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket.
command {
set -e
mkdir -p "$(dirname ~{outputVcfPath})"
@@ -575,7 +850,7 @@ task MergeVCFs {
OUTPUT=~{outputVcfPath} \
COMPRESSION_LEVEL=~{compressionLevel} \
USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
- USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
+ USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
}
output {
@@ -584,9 +859,9 @@ task MergeVCFs {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -594,16 +869,17 @@ task MergeVCFs {
inputVCFs: {description: "The VCF files to be merged.", category: "required"}
inputVCFsIndexes: {description: "The indexes of the VCF files.", category: "required"}
outputVcfPath: {description: "The location the output VCF file should be written to.", category: "required"}
-
- memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
- timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
- compressionLevel: {description: "The compression level at which the BAM files are written", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "Multiple variant files combined into a single variant file."}
+ outputVcfIndex: {description: "Index of `outputVcf`."}
}
}
@@ -613,10 +889,12 @@ task SamToFastq {
File inputBamIndex
Boolean paired = true
- String memory = "17G"
String javaXmx = "16G" # High memory default to avoid crashes.
- String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
- File? NONE
+ String memory = "17GiB"
+ Int timeMinutes = 30
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
+
+ File? noneFile
}
String outputRead1 = basename(inputBam, "\.[bs]am") + "_R1.fastq.gz"
@@ -635,13 +913,36 @@ task SamToFastq {
output {
File read1 = outputRead1
- File? read2 = if paired then outputRead2 else NONE
- File? unpairedRead = if paired then outputUnpaired else NONE
+ File? read2 = if paired then outputRead2 else noneFile
+ File? unpairedRead = if paired then outputUnpaired else noneFile
}
runtime {
- docker: dockerImage
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputBam: {description: "Input BAM file to extract reads from.", category: "required"}
+ inputBamIndex: {description: "Input BAM index file.", category: "required"}
+ paired: {description: "Set to false when input data is single-end.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ read1: {description: "Fastq file containing reads from the first pair."}
+ read2: {description: "Fastq file containing reads from the second pair."}
+ unpairedRead: {description: "Fastq file containing unpaired reads."}
+ }
+
+ meta {
+ WDL_AID: {
+ exclude: ["noneFile"]
+ }
}
}
@@ -650,9 +951,9 @@ task ScatterIntervalList {
File interval_list
Int scatter_count
- String memory = "4G"
String javaXmx = "3G"
- String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+ String memory = "4GiB"
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
}
command {
@@ -674,8 +975,8 @@ task ScatterIntervalList {
}
runtime {
- docker: dockerImage
memory: memory
+ docker: dockerImage
}
}
@@ -687,13 +988,15 @@ task SortSam {
Boolean createMd5File = false
Int maxRecordsInRam = 500000
Int compressionLevel = 1
+ Boolean useJdkInflater = false
+ Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
- # Default ram of 4 GB. Using 125001.0 to prevent an answer of
+ # Default ram of 4 GB. Using 125001.0 to prevent an answer of
# 4.000000001 which gets rounded to 5.
# GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778
Int XmxGb = ceil(maxRecordsInRam / 125001.0)
- Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
- String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+ Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 3)
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
}
command {
@@ -706,6 +1009,8 @@ task SortSam {
SORT_ORDER=~{true="queryname" false="coordinate" sortByName} \
CREATE_INDEX=true \
COMPRESSION_LEVEL=~{compressionLevel} \
+ USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
+ USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater} \
VALIDATION_STRINGENCY=SILENT \
CREATE_MD5_FILE=~{true="true" false="false" createMd5File}
@@ -718,19 +1023,28 @@ task SortSam {
runtime {
cpu: 1
- memory: "~{1 + XmxGb}G"
+ memory: "~{1 + XmxGb}GiB"
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- inputBam: {description: "The unsorted input BAM file", category: "required"}
+ # inputs
+ inputBam: {description: "The unsorted input BAM file.", category: "required"}
outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
- XmxGb: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.",
- category: "advanced"}
+ sortByName: {description: "Sort the output file by name, default is position.", category: "advanced"}
+ createMd5File: {description: "Whether to create an MD5 digest for any BAM or FASTQ files created.", category: "advanced"}
+ maxRecordsInRam: {description: "This will specify the number of records stored in RAM before spilling to disk.", category: "advanced"}
+ compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
+ useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
+ useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
+ XmxGb: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: "Sorted BAM file."}
+ outputBamIndex: {description: "Index of sorted BAM file."}
}
}
@@ -738,12 +1052,13 @@ task SortVcf {
input {
Array[File]+ vcfFiles
String outputVcfPath
+
File? dict
- String memory = "9G"
String javaXmx = "8G"
- Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5)
- String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
+ String memory = "9GiB"
+ Int timeMinutes = 1 + ceil(size(vcfFiles, "GiB") * 5)
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
}
@@ -763,9 +1078,9 @@ task SortVcf {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -773,13 +1088,14 @@ task SortVcf {
vcfFiles: {description: "The VCF files to merge and sort.", category: "required"}
outputVcfPath: {description: "The location the sorted VCF files should be written to.", category: "required"}
dict: {description: "A sequence dictionary matching the VCF files.", category: "advanced"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "Sorted VCF file(s)."}
+ outputVcfIndex: {description: "Index(es) of sort(ed) VCF file(s)."}
}
}
@@ -788,10 +1104,11 @@ task RenameSample {
File inputVcf
String outputPath = "./picard/renamed.vcf"
String newSampleName
- String memory = "9G"
+
String javaXmx = "8G"
- Int timeMinutes = 1 + ceil(size(inputVcf, "G") * 2)
- String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
+ String memory = "9GiB"
+ Int timeMinutes = 1 + ceil(size(inputVcf, "GiB") * 2)
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
}
command {
@@ -809,9 +1126,9 @@ task RenameSample {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -819,9 +1136,87 @@ task RenameSample {
inputVcf: {description: "The VCF file to process.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
newSampleName: {description: "A string to replace the old sample name.", category: "required"}
- memory: {description: "The memory required to run the programs", category: "advanced"}
- javaXmx: {description: "The max. memory allocated for JAVA", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ renamedVcf: {description: "New VCF with renamed sample."}
}
}
+
+task UmiAwareMarkDuplicatesWithMateCigar {
+ input {
+ Array[File] inputBams
+ String outputPath
+ String outputPathMetrics = outputPath + ".metrics"
+ String outputPathUmiMetrics = outputPath + ".umi-metrics"
+ Int maxRecordsInRam = 1500000 # Default is 500_000 but that will lead to very small files on disk.
+ String? assumeSortOrder
+ String tempdir = "temp"
+ Boolean removeDuplicates = true
+ String umiTagName = "RX"
+ Int compressionLevel = 1
+ Boolean useJdkInflater = false
+ Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
+ String javaXmx = "8G"
+ String memory = "9GiB"
+ Int timeMinutes = 360
+ String dockerImage = "quay.io/biocontainers/picard:3.3.0--hdfd78af_0"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPath})" ~{tempdir}
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ UmiAwareMarkDuplicatesWithMateCigar \
+ INPUT=~{sep=' INPUT=' inputBams} \
+ O=~{outputPath} \
+ M=~{outputPathMetrics} \
+ UMI_TAG_NAME=~{umiTagName} \
+ UMI_METRICS_FILE=~{outputPathUmiMetrics} \
+ TMP_DIR=~{tempdir} \
+ REMOVE_DUPLICATES=~{removeDuplicates} \
+ MAX_RECORDS_IN_RAM=~{maxRecordsInRam} \
+ CREATE_INDEX=true \
+ COMPRESSION_LEVEL=~{compressionLevel} \
+ USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
+ USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater} \
+ ~{"ASSUME_SORT_ORDER=" + assumeSortOrder}
+ }
+
+ output {
+ File outputBam = outputPath
+ File outputBamIndex = sub(outputPath, "\.bam$", ".bai")
+ File outputMetrics = outputPathMetrics
+ File outputUmiMetrics = outputPathUmiMetrics
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputBams: {description: "The BAM files for which the duplicate reads should be marked.", category: "required"}
+ outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
+ outputPathMetrics: {description: "The location the output metrics file should be written to.", category: "required"}
+ outputPathUmiMetrics: {description: "The location the output UMI metrics file should be written to.", category: "required"}
+ removeDuplicates: {description: "Whether the duplicate reads should be removed instead of marked.", category: "common"}
+ umiTagName: {description: "Which tag in the BAM file holds the UMI.", category: "common"}
+ assumeSortOrder: {description: "Assume a certain sort order even though the header might say otherwise.", category: "common"}
+ tempdir: {description: "Temporary directory.", category: "advanced"}
+ compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
+ maxRecordsInRam: {description: "This will specify the number of records stored in RAM before spilling to disk.", category: "advanced"}
+ useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
+ useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ }
+}
\ No newline at end of file
diff --git a/prepareShiny.wdl b/prepareShiny.wdl
new file mode 100644
index 00000000..28910743
--- /dev/null
+++ b/prepareShiny.wdl
@@ -0,0 +1,106 @@
+version 1.0
+
+# Copyright (c) 2017 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task CreateDesignMatrix {
+ input {
+ File countTable
+ String shinyDir = "."
+
+ String memory = "5GiB"
+ Int timeMinutes = 30
+ String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{shinyDir}
+ predex design \
+ --input ~{countTable} \
+ --output ~{shinyDir}
+ }
+
+ output {
+ File dgeDesign = shinyDir + "/design_matrix.tsv"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ countTable: {description: "The created count table from HTseq.", category: "required"}
+ shinyDir: {description: "The directory to write the output to.", category: "required"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ dgeDesign: {description: "Design matrix template to add sample information for DGE analysis."}
+ }
+}
+
+task CreateAnnotation {
+ input {
+ File referenceFasta
+ File referenceGtfFile
+ String shinyDir = "."
+
+ String memory = "5GiB"
+ Int timeMinutes = 30
+ String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{shinyDir}
+ predex annotation \
+ --fasta ~{referenceFasta} \
+ --gtf ~{referenceGtfFile} \
+ --output ~{shinyDir}
+ }
+
+ output {
+ File dgeAnnotation = shinyDir + "/annotation.tsv"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ referenceFasta: {description: "The reference Fasta file.", category: "required"}
+ referenceGtfFile: {description: "The reference GTF file.", category: "required"}
+ shinyDir: {description: "The directory to write the output to.", category: "required"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ dgeAnnotation: {description: "Annotation file for DGE analysis."}
+ }
+}
diff --git a/requirements-test.txt b/requirements-test.txt
deleted file mode 100644
index f074413b..00000000
--- a/requirements-test.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-cromwell
-miniwdl
\ No newline at end of file
diff --git a/rtg.wdl b/rtg.wdl
index 104a5ef9..62e1e77f 100644
--- a/rtg.wdl
+++ b/rtg.wdl
@@ -22,13 +22,13 @@ version 1.0
task Format {
input {
- String format = "fasta"
- String outputPath = "seq_data.sdf"
Array[File]+ inputFiles
- String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
+ String format = "fasta"
+ String outputPath = "reference_data"
String rtgMem = "8G"
- String memory = "9G"
- Int timeMinutes = 1 + ceil(size(inputFiles) * 2)
+ String memory = "9GiB"
+ Int timeMinutes = 1 + ceil(size(inputFiles, "GiB") * 2)
+ String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
}
command {
@@ -40,25 +40,27 @@ task Format {
}
output {
- File sdf = outputPath
+ Array[File] referenceFiles = glob("~{outputPath}/*")
}
runtime {
- docker: dockerImage
memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- format: {description: "Format of input. Allowed values are [fasta, fastq, fastq-interleaved, sam-se, sam-pe].",
- category: "advanced"}
+ # inputs
+ inputFiles: {description: "Input sequence files. May be specified 1 or more times.", category: "required"}
+ format: {description: "Format of input. Allowed values are [fasta, fastq, fastq-interleaved, sam-se, sam-pe].", category: "advanced"}
outputPath: {description: "Where the output should be placed.", category: "advanced"}
- inputFiles: {description: "input sequence files. May be specified 1 or more times.", category: "required"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
- timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ rtgMem: {description: "The amount of memory rtg will allocate to the JVM.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- rtgMem: {description: "The amount of memory rtg will allocate to the JVM", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ referenceFiles: {description: "An array with all the generated reference files"}
}
}
@@ -68,20 +70,22 @@ task VcfEval {
File baselineIndex
File calls
File callsIndex
- File? evaluationRegions
- File? bedRegions
+ Boolean squashPloidy = false
+ String outputMode = "split"
String outputDir = "output/"
- File template
+ Array[File] referenceFiles
Boolean allRecords = false
Boolean decompose = false
Boolean refOverlap = false
+
+ File? evaluationRegions
+ File? bedRegions
String? sample
- Boolean squashPloidy = false
- String outputMode = "split"
- Int threads = 1 # tool default is number of cores in the system 😱
+
String rtgMem = "8G"
- String memory = "9G"
- Int timeMinutes = 1 + ceil(size([baseline, calls], "G") * 5)
+ Int threads = 1 # Tool default is number of cores in the system 😱.
+ String memory = "9GiB"
+ Int timeMinutes = 1 + ceil(size([baseline, calls], "GiB") * 5)
String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
}
@@ -94,7 +98,7 @@ task VcfEval {
~{"--evaluation-regions " + evaluationRegions} \
~{"--bed-regions " + bedRegions} \
--output ~{outputDir} \
- --template ~{template} \
+ --template $(dirname ~{referenceFiles[0]}) \
~{true="--all-records" false="" allRecords} \
~{true="--decompose" false="" decompose} \
~{true="--ref-overlap" false="" refOverlap} \
@@ -132,39 +136,47 @@ task VcfEval {
}
runtime {
- docker: dockerImage
cpu: threads
memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- baseline: {description: "VCF file containing baseline variants", category: "required"}
- baselineIndex: {description: "The baseline's VCF index", category: "required"}
- calls: {description: "VCF file containing called variants", category: "required"}
- callsIndex: {description: "The call's VCF index", category: "required"}
- outputDir: {description: "Directory for output", category: "advanced"}
- bedRegions: {description: "if set, only read VCF records that overlap the ranges contained in the specified BED file", category: "advanced"}
- evaluationRegions: {description: "if set, evaluate within regions contained in the supplied BED file, allowing transborder matches. To be used for truth-set high-confidence regions or other regions of interest where region boundary effects should be minimized",
- category: "advanced"}
- template: {description: "SDF of the reference genome the variants are called against", category: "required"}
- allRecords: {description: "use all records regardless of FILTER status (Default is to only process records where FILTER is \".\" or \"PASS\")",
- category: "common"}
- decompose: {description: "decompose complex variants into smaller constituents to allow partial credit", category: "common"}
- refOverlap: {description: "allow alleles to overlap where bases of either allele are same-as-ref (Default is to only allow VCF anchor base overlap)",
- category: "common"}
- sample: {description: "the name of the sample to select. Use , to select different sample names for baseline and calls. (Required when using multi-sample VCF files)",
- category: "common"}
- squashPloidy: {description: "treat heterozygous genotypes as homozygous ALT in both baseline and calls, to allow matches that ignore zygosity differences",
- category: "common"}
- outputMode: {description: "output reporting mode. Allowed values are [split, annotate, combine, ga4gh, roc-only] (Default is split)",
- category: "advanced"}
- threads: {description: "Number of threads. Default is 1", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
- timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- rtgMem: {description: "The amount of memory rtg will allocate to the JVM", category: "advanced"}
+ # inputs
+ baseline: {description: "VCF file containing baseline variants.", category: "required"}
+ baselineIndex: {description: "The baseline's VCF index.", category: "required"}
+ calls: {description: "VCF file containing called variants.", category: "required"}
+ callsIndex: {description: "The call's VCF index.", category: "required"}
+ squashPloidy: {description: "treat heterozygous genotypes as homozygous ALT in both baseline and calls, to allow matches that ignore zygosity differences.", category: "common"}
+ outputMode: {description: "output reporting mode. Allowed values are [split, annotate, combine, ga4gh, roc-only] (Default is split).", category: "advanced"}
+ outputDir: {description: "Directory for output.", category: "advanced"}
+ referenceFiles: {description: "An array of reference Files generated by the Format task.", category: "required"}
+ allRecords: {description: "use all records regardless of FILTER status (Default is to only process records where FILTER is \".\" or \"PASS\").", category: "common"}
+ decompose: {description: "decompose complex variants into smaller constituents to allow partial credit.", category: "common"}
+ refOverlap: {description: "allow alleles to overlap where bases of either allele are same-as-ref (Default is to only allow VCF anchor base overlap).", category: "common"}
+ sample: {description: "the name of the sample to select. Use , to select different sample names for baseline and calls. (Required when using multi-sample VCF files).", category: "common"}
+ bedRegions: {description: "if set, only read VCF records that overlap the ranges contained in the specified BED file.", category: "advanced"}
+ evaluationRegions: {description: "if set, evaluate within regions contained in the supplied BED file, allowing transborder matches. To be used for truth-set high-confidence regions or other regions of interest where region boundary effects should be minimized.", category: "advanced"}
+ rtgMem: {description: "The amount of memory rtg will allocate to the JVM.", category: "advanced"}
+ threads: {description: "Number of threads. Default is 1.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ falseNegativesVcf: {description: "Variants from thebaselineVCF which were not correctly called."}
+ falseNegativesVcfIndex: {description: "Index of the output VCF file `falseNegativesVcf`."}
+ falsePositivesVcf: {description: "Variants from thecallsVCF which do not agree with baseline variants."}
+ falsePositivesVcfIndex: {description: "Index of the output VCF file `falsePositivesVcf`."}
+ summary: {description: "Summary statistic file."}
+ truePositivesBaselineVcf: {description: "Variants from thebaselineVCF which agree with variants in thecalls VCF."}
+ truePositivesBaselineVcfIndex: {description: "Index of the output VCF file `truePositivesBaselineVcf`."}
+ truePositivesVcf: {description: "Variants from thecallsVCF which agree with variants in the baseline VCF."}
+ truePositivesVcfIndex: {description: "Index of the output VCF file `truePositivesVcf`."}
+ nonSnpRoc: {description: "ROC data derived from those variants which were not represented asSNPs."}
+ phasing: {description: "Phasing file."}
+ weightedRoc: {description: "ROC data derived from all analyzed call variants, regardless of their representation."}
+ allStats: {description: "All output files combined in a array."}
}
}
-
diff --git a/sambamba.wdl b/sambamba.wdl
index cd8da21e..be347f94 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -20,29 +20,74 @@ version 1.0
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
+task Flagstat {
+ input {
+ File inputBam
+ File inputBamIndex
+ String outputPath = "./flagstat.txt"
+
+ Int threads = 2
+ String memory = "8GiB"
+ Int timeMinutes = 320
+ String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
+ }
+
+ command {
+ sambamba flagstat \
+ -t ~{threads} \
+ ~{inputBam} \
+ > ~{outputPath}
+ }
+
+ output {
+ File stats = outputPath
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputBam: {description: "The input BAM file.", category: "required"}
+ inputBamIndex: {description: "The index for the BAM file.", category: "required"}
+ outputPath: {description: "The path to write the ouput to.", category: "required"}
+
+ threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ }
+}
+
task Markdup {
input {
Array[File] inputBams
String outputPath
- # Sambamba scales like this: 1 thread is fully utilized (1). 2 threads 1.8 utilized. 3 -> 2.4, 4-> 2.7.
- # 2 threads reduces wall clock time by more than 40%.
- Int threads = 2
Int compressionLevel = 1
+ # sortBufferSize and ioBufferSize taken from markdup defaults as of sambamba 0.7.1.
+ Int sortBufferSize = 4096
+ Int ioBufferSize = 128
+ Boolean removeDuplicates = false
+
Int? hashTableSize
Int? overFlowListSize
- # sortBufferSize and ioBufferSize taken from markdup defaults as of sambamba 0.7.1
- Int sortBufferSize = 2048
- Int ioBufferSize = 128
- Boolean removeDuplicates = false
+ # Sambamba scales like this: 1 thread is fully utilized (1).
+ # 2 threads 1.8 utilized. 3 -> 2.4, 4-> 2.7.
+ # 2 threads reduces wall clock time by more than 40%.
+ Int threads = 2
# According to the manual sambamba markdup uses the sortbufferSize + 2 times the ioBuffer size.
- # Added 1024 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
- Int memoryMb = 1024 + sortBufferSize + 2 * ioBufferSize
- String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
+ # Added 8192 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
+ Int memoryMb = 8192 + sortBufferSize + 2 * ioBufferSize
# Time minute calculation does not work well for higher number of threads.
- Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8) / threads
+ Int timeMinutes = 1 + ceil(size(inputBams, "GiB") * 25) / threads
+ String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
}
+
String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
command {
@@ -57,7 +102,7 @@ task Markdup {
~{"--sort-buffer-size " + sortBufferSize} \
~{"--io-buffer-size " + ioBufferSize} \
~{sep=' ' inputBams} ~{outputPath}
- # sambamba creates an index for us
+ # sambamba creates an index for us.
mv ~{outputPath}.bai ~{bamIndexPath}
}
@@ -67,8 +112,8 @@ task Markdup {
}
runtime {
- memory: "~{memoryMb}M"
cpu: threads
+ memory: "~{memoryMb}MiB"
time_minutes: timeMinutes
docker: dockerImage
}
@@ -78,17 +123,19 @@ task Markdup {
inputBams: {description: "The input BAM files.", category: "required"}
outputPath: {description: "Output directory path + output file.", category: "required"}
compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
- memoryMb: {description: "The amount of memory available to the job in megabytes.", category: "advanced"}
- removeDuplicates: {description: "Whether to remove the duplicates (instead of only marking them).", category: "advanced"}
- hashTableSize: {description: "Sets sambamba's hash table size", category: "advanced"}
- overFlowListSize: {description: "Sets sambamba's overflow list size", category: "advanced"}
- sortBufferSize: {description: "The amount of mb allocated to the sort buffer", category: "advanced"}
+ sortBufferSize: {description: "The amount of mb allocated to the sort buffer.", category: "advanced"}
ioBufferSize: {description: "The amount of mb allocated to each IO buffer. Sambamba uses two IO buffers.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ removeDuplicates: {description: "Whether to remove the duplicates (instead of only marking them).", category: "advanced"}
+ hashTableSize: {description: "Sets sambamba's hash table size.", category: "advanced"}
+ overFlowListSize: {description: "Sets sambamba's overflow list size.", category: "advanced"}
threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
+ memoryMb: {description: "The amount of memory available to the job in megabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
# outputs
outputBam: {description: "Sorted BAM file."}
+ outputBamIndex: {description: "Sorted BAM file index."}
}
}
@@ -98,14 +145,15 @@ task Sort {
String outputPath = basename(inputBam, "\.bam") + ".sorted.bam"
Boolean sortByName = false
Int compressionLevel = 1
- Int threads = 1
+
Int memoryPerThreadGb = 4
+ Int threads = 1
Int memoryGb = 1 + threads * memoryPerThreadGb
+ Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 3)
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
- Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
}
- # Select first needed as outputPath is optional input. (bug in cromwell)
+ # Select first needed as outputPath is optional input (bug in cromwell).
String bamIndexPath = sub(select_first([outputPath]), "\.bam$", ".bai")
command {
@@ -118,7 +166,7 @@ task Sort {
-m ~{memoryPerThreadGb}G \
-o ~{outputPath} \
~{inputBam}
- # sambamba creates an index for us
+ # sambamba creates an index for us.
mv ~{outputPath}.bai ~{bamIndexPath}
}
@@ -129,7 +177,7 @@ task Sort {
runtime {
cpu: threads
- memory: "~{memoryGb}G"
+ memory: "~{memoryGb}GiB"
docker: dockerImage
time_minutes: timeMinutes
}
@@ -140,12 +188,14 @@ task Sort {
outputPath: {description: "Output directory path + output file.", category: "required"}
sortByName: {description: "Sort the inputBam by read name instead of position.", category: "advanced"}
compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
- memoryGb: {description: "The amount of memory available to the job in gigabytes.", category: "advanced"}
- memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes.", category: "advanced"}
threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
+ memoryGb: {description: "The amount of memory available to the job in gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
# outputs
outputBam: {description: "Sorted BAM file."}
+ outputBamIndex: {description: "Sorted BAM file index."}
}
-}
\ No newline at end of file
+}
diff --git a/samtools.wdl b/samtools.wdl
index c155f026..711cb906 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -24,10 +24,13 @@ task BgzipAndIndex {
input {
File inputFile
String outputDir
- String type = "vcf"
+ String preset = "vcf"
- Int timeMinutes = 1 + ceil(size(inputFile, "G"))
- String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
+ Int compressLevel = 1
+ Int threads = 1
+ String memory = "2GiB"
+ Int timeMinutes = 1 + ceil(size(inputFile, "GiB"))
+ String dockerImage = "quay.io/biocontainers/htslib:1.21--h566b1c6_1"
}
String outputGz = outputDir + "/" + basename(inputFile) + ".gz"
@@ -35,8 +38,15 @@ task BgzipAndIndex {
command {
set -e
mkdir -p "$(dirname ~{outputGz})"
- bgzip -c ~{inputFile} > ~{outputGz}
- tabix ~{outputGz} -p ~{type}
+ bgzip \
+ --threads ~{threads} \
+ --compress-level ~{compressLevel} \
+ -c ~{inputFile} > ~{outputGz}
+
+ tabix \
+ --preset ~{preset} \
+ --threads ~{threads - 1} \
+ ~{outputGz}
}
output {
@@ -45,6 +55,8 @@ task BgzipAndIndex {
}
runtime {
+ cpu: threads
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
@@ -53,10 +65,61 @@ task BgzipAndIndex {
# inputs
inputFile: {description: "The file to be compressed and indexed.", category: "required"}
outputDir: {description: "The directory in which the output will be placed.", category: "required"}
- type: {description: "The type of file (eg. vcf or bed) to be compressed and indexed.", category: "common"}
+ preset: {description: "The preset for the file (eg. vcf or bed) to be compressed and indexed.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ compressLevel: {description: "Set compression level.", category: "advanced"}
+ threads: {description: "The number of threads to use.", category: "advanced"}
+
+ # outputs
+ compressed: {description: "Compressed input file."}
+ index: {description: "Index of the compressed input file."}
+ }
+}
+
+task DictAndFaidx {
+ input {
+ File inputFile
+ String memory = "3GiB"
+ Int timeMinutes = 5 + ceil(size(inputFile, "GiB") * 5)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
+ }
+
+ String outputFile = basename(inputFile)
+ # Capture .fa¸ .fna and .fasta
+ String outputDict = sub(outputFile, "\.fn?as?t?a?$", "") + ".dict"
+ # This executes both dict and faidx, so indexes are co-located in the same folder.
+ command <<<
+ set -e
+ cp ~{inputFile} ~{outputFile}
+ samtools dict -o ~{outputDict} ~{outputFile}
+ samtools faidx ~{outputFile} --fai-idx ~{outputFile}.fai
+ >>>
+
+ output {
+ File outputFasta = outputFile
+ File outputFastaDict = outputDict
+ File outputFastaFai = outputFile + ".fai"
+ }
+
+ runtime {
+ memory: memory
+ docker: dockerImage
+ time_minutes: timeMinutes
+ cpu: 1
+ }
+
+ parameter_meta {
+ # inputs
+ inputFile: {description: "The input fasta file.", category: "required"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ # outputs
+ outputFasta: {description: "Fasta file that is co-located with the indexes"}
+ outputFastaFai: {description: "Fasta index file for the outputFasta file."}
+ outputFastaDict: {description: "Sequence dictionary for the outputFasta file."}
}
}
@@ -65,8 +128,8 @@ task Faidx {
File inputFile
String outputDir
- String memory = "2G"
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ String memory = "2GiB"
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
command {
@@ -104,38 +167,44 @@ task Fastq {
String outputRead1
String? outputRead2
String? outputRead0
+ String? outputReadS
+ Boolean appendReadNumber = false
+ Boolean outputQuality = false
+
Int? includeFilter
Int? excludeFilter
Int? excludeSpecificFilter
- Boolean appendReadNumber = false
- Boolean outputQuality = false
- Int? compressionLevel
+ Int compressionLevel = 1
Int threads = 1
- String memory = "1G"
- Int timeMinutes = 1 + ceil(size(inputBam) * 2)
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ String memory = "1GiB"
+ Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 2)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
command {
+ set -e
+ mkdir -p "$(dirname ~{outputRead1})"
+ samtools collate -u -O ~{inputBam} | \
samtools fastq \
- ~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
+ ~{"-1 " + outputRead1} \
~{"-2 " + outputRead2} \
~{"-0 " + outputRead0} \
+ ~{"-s " + outputReadS} \
~{"-f " + includeFilter} \
~{"-F " + excludeFilter} \
~{"-G " + excludeSpecificFilter} \
~{true="-N" false="-n" appendReadNumber} \
~{true="-O" false="" outputQuality} \
- ~{"-c " + compressionLevel} \
- ~{"--threads " + threads} \
- ~{inputBam}
+ -c ~{compressionLevel} \
+ "--threads " ~{threads - 1}
}
output {
File read1 = outputRead1
File? read2 = outputRead2
File? read0 = outputRead0
+ File? readS = outputReadS
}
runtime {
@@ -151,16 +220,22 @@ task Fastq {
outputRead1: {description: "The location the reads (first reads for pairs, in case of paired-end sequencing) should be written to.", category: "required"}
outputRead2: {description: "The location the second reads from pairs should be written to.", category: "common"}
outputRead0: {description: "The location the unpaired reads should be written to (in case of paired-end sequenicng).", category: "advanced"}
- includeFilter: {description: "Include reads with ALL of these flags. Corresponds to `-f`", category: "advanced"}
- excludeFilter: {description: "Exclude reads with ONE OR MORE of these flags. Corresponds to `-F`", category: "advanced"}
- excludeSpecificFilter: {description: "Exclude reads with ALL of these flags. Corresponds to `-G`", category: "advanced"}
- appendReadNumber: {description: "Append /1 and /2 to the read name, or don't. Corresponds to `-n/N`", category: "advanced"}
+ outputReadS: {description: "The location singleton reads should be written to.", category: "advanced"}
+ appendReadNumber: {description: "Append /1 and /2 to the read name, or don't. Corresponds to `-n/N`.", category: "advanced"}
outputQuality: {description: "Equivalent to samtools fastq's `-O` flag.", category: "advanced"}
+ includeFilter: {description: "Include reads with ALL of these flags. Corresponds to `-f`.", category: "advanced"}
+ excludeFilter: {description: "Exclude reads with ONE OR MORE of these flags. Corresponds to `-F`.", category: "advanced"}
+ excludeSpecificFilter: {description: "Exclude reads with ALL of these flags. Corresponds to `-G`.", category: "advanced"}
+ compressionLevel: {description: "Set compression level when writing gz or bgzf fastq files.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ read1: {description: "Reads with the READ1 FLAG set."}
+ read2: {description: "Reads with the READ2 FLAG set."}
+ read0: {description: "Reads with either READ1 FLAG or READ2 flag set."}
}
}
@@ -168,9 +243,10 @@ task FilterShortReadsBam {
input {
File bamFile
String outputPathBam
- String memory = "1G"
- Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8)
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+
+ String memory = "1GiB"
+ Int timeMinutes = 1 + ceil(size(bamFile, "GiB") * 8)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
@@ -196,11 +272,16 @@ task FilterShortReadsBam {
}
parameter_meta {
+ # inputs
bamFile: {description: "The bam file to process.", category: "required"}
outputPathBam: {description: "The filtered bam file.", category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ filteredBam: {description: "BAM file filtered for short reads."}
+ filteredBamIndex: {description: "Index of filtered BAM file."}
}
}
@@ -209,15 +290,20 @@ task Flagstat {
File inputBam
String outputPath
- String memory = "256M" # Only 40.5 MiB used for 150G bam file.
+ Int threads = 1
+
+ String memory = "256MiB" # Only 40.5 MiB used for 150G bam file.
Int timeMinutes = 1 + ceil(size(inputBam, "G"))
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- samtools flagstat ~{inputBam} > ~{outputPath}
+
+ samtools flagstat \
+ --threads ~{threads - 1} \
+ ~{inputBam} > ~{outputPath}
}
output {
@@ -225,6 +311,7 @@ task Flagstat {
}
runtime {
+ cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
@@ -236,18 +323,25 @@ task Flagstat {
outputPath: {description: "The location the ouput should be written to.", category: "required"}
memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ threads: {description: "The number of threads to use.", category: "advanced"}
+
+ # outputs
+ flagstat: {description: "The number of alignments for each FLAG type."}
}
}
task Index {
input {
File bamFile
+
String? outputBamPath
- String memory = "2G"
- Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+
+ Int threads = 1
+
+ String memory = "2GiB"
+ Int timeMinutes = 1 + ceil(size(bamFile, "GiB") * 4)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
# Select_first is needed, otherwise womtool validate fails.
@@ -261,9 +355,11 @@ task Index {
if [ ! -f ~{outputPath} ]
then
mkdir -p "$(dirname ~{outputPath})"
- ln ~{bamFile} ~{outputPath}
+ ln ~{bamFile} ~{outputPath} || cp ~{bamFile} ~{outputPath}
fi
- samtools index ~{outputPath} ~{bamIndexPath}
+ samtools index \
+ --threads ~{threads -1} \
+ ~{outputPath} ~{bamIndexPath}
'
}
@@ -273,6 +369,7 @@ task Index {
}
runtime {
+ cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
@@ -281,12 +378,15 @@ task Index {
parameter_meta {
# inputs
bamFile: {description: "The BAM file for which an index should be made.", category: "required"}
- outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.",
- category: "common"}
+ outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.", category: "common"}
memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ threads: {description: "The number of threads to use.", category: "advanced"}
+
+ # outputs
+ indexedBam: {description: "BAM file that was indexed."}
+ index: {description: "Index of the input BAM file."}
}
}
@@ -294,15 +394,18 @@ task Markdup {
input {
File inputBam
String outputBamPath
+ Int threads = 1
- Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 2)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
command {
set -e
mkdir -p "$(dirname ~{outputBamPath})"
- samtools markdup ~{inputBam} ~{outputBamPath}
+ samtools markdup \
+ --threads ~{threads - 1} \
+ ~{inputBam} ~{outputBamPath}
}
output {
@@ -310,6 +413,7 @@ task Markdup {
}
runtime {
+ cpu: threads
docker: dockerImage
time_minutes: timeMinutes
}
@@ -319,8 +423,11 @@ task Markdup {
inputBam: {description: "The BAM file to be processed.", category: "required"}
outputBamPath: {description: "The location of the output BAM file.", category: "required"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ threads: {description: "The number of threads to use.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: "BAM file with duplicate alignments marked."}
}
}
@@ -329,11 +436,18 @@ task Merge {
Array[File]+ bamFiles
String outputBamPath = "merged.bam"
Boolean force = true
- Int threads = 1
- Int timeMinutes = 1 + ceil(size(bamFiles, "G") * 2)
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ Boolean combineRGHeaders = false
+ Boolean combinePGHeaders = false
+
+ Int compressionLevel = 1
+ # Use one thread per input + one for the output + one for merging
+ Int threads = length(bamFiles) + 2
+ String memory = "4GiB"
+ Int timeMinutes = 1 + ceil(size(bamFiles, "GiB") * 4)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
+
String indexPath = sub(outputBamPath, "\.bam$",".bai")
# Samtools uses additional threads for merge.
@@ -343,8 +457,11 @@ task Merge {
samtools merge \
--threads ~{threads - 1} \
~{true="-f" false="" force} \
+ -l ~{compressionLevel} \
+ ~{true="-c" false="" combineRGHeaders} \
+ ~{true="-p" false="" combinePGHeaders} \
~{outputBamPath} ~{sep=' ' bamFiles}
- samtools index ~{outputBamPath} ~{indexPath}
+ samtools index -@ ~{threads - 1} ~{outputBamPath} ~{indexPath}
}
output {
@@ -354,8 +471,9 @@ task Merge {
runtime {
cpu: threads
- docker: dockerImage
+ memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -363,9 +481,54 @@ task Merge {
bamFiles: {description: "The BAM files to merge.", category: "required"}
outputBamPath: {description: "The location the merged BAM file should be written to.", category: "common"}
force: {description: "Equivalent to samtools merge's `-f` flag.", category: "advanced"}
+
+ combineRGHeaders: {description: "Combine @RG headers with colliding IDs", category: "advanced"}
+ combinePGHeaders: {description: "Combine @PG headers with colliding IDs", category: "advanced"}
+
+ compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
+
+ threads: {description: "Number of threads to use.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: "Multiple BAM files merged into one."}
+ outputBamIndex: {description: "Index of the merged BAM file."}
+ }
+}
+
+task Quickcheck {
+ input {
+ File inputBam
+
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
+ }
+
+ command {
+ set -e
+ samtools quickcheck ~{inputBam}
+ }
+
+ output {
+ File outputBam = inputBam
+ }
+
+ runtime {
+ cpu: 1
+ time_minutes: 5
+ memory: "1GiB"
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputBam: {description: "The input BAM/SAM/CRAM file.", category: "required"}
+
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: "The exact same input file, but use this so it is recognised as a dependent task."}
}
}
@@ -375,14 +538,15 @@ task Sort {
String outputPath = basename(inputBam, "\.bam") + ".sorted.bam"
Boolean sortByName = false
Int compressionLevel = 1
- Int threads = 1
+
Int memoryPerThreadGb = 4
+ Int threads = 1
Int memoryGb = 1 + threads * memoryPerThreadGb
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
- Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
+ Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 3)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
- # Select first needed as outputPath is optional input. (bug in cromwell)
+ # Select first needed as outputPath is optional input (bug in cromwell).
String bamIndexPath = sub(select_first([outputPath]), "\.bam$", ".bai")
command {
@@ -396,7 +560,7 @@ task Sort {
-o ~{outputPath} \
~{inputBam}
samtools index \
- -@ ~{threads} \
+ --threads ~{threads - 1} \
~{outputPath} ~{bamIndexPath}
}
@@ -406,10 +570,10 @@ task Sort {
}
runtime {
- cpu: 1
- memory: "~{memoryGb}G"
- docker: dockerImage
+ cpu: threads
+ memory: "~{memoryGb}GiB"
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -418,34 +582,97 @@ task Sort {
outputPath: {description: "Output directory path + output file.", category: "required"}
sortByName: {description: "Sort the inputBam by read name instead of position.", category: "advanced"}
compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
+ memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes.", category: "advanced"}
+ threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
memoryGb: {description: "The amount of memory available to the job in gigabytes.", category: "advanced"}
- memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
- threads: {description: "The number of additional threads that will be used for this task.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
outputBam: {description: "Sorted BAM file."}
+ outputBamIndex: {description: "Sorted BAM file index."}
+ }
+}
+
+task Split {
+ input {
+ File inputBam
+ String outputPath
+ String? unaccountedPath
+ String filenameFormat = "%!.%."
+
+ Int compressionLevel = 1
+
+ Int threads = 1
+ String memory = "1GiB"
+ Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 2)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
+ }
+
+ command {
+ set -e
+ mkdir -p "~{outputPath}/rg/"
+
+ samtools split \
+ --output-fmt bam \
+ --output-fmt-option level=~{compressionLevel} \
+ -f "~{outputPath}/rg/~{filenameFormat}" \
+ ~{"-u " + unaccountedPath} \
+ --threads ~{threads - 1} \
+ --write-index \
+ ~{inputBam}
+ }
+
+ output {
+ Array[File] splitBam = glob(outputPath + "/rg/*.bam")
+ Array[File] splitBamIndex = glob(outputPath + "/rg/*.bam.csi")
+ File? unaccounted = unaccountedPath
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ docker: dockerImage
+ time_minutes: timeMinutes
+ }
+
+ parameter_meta {
+ # inputs
+ inputBam: {description: "The bam file to split.", category: "required"}
+ outputPath: {description: "Directory to store output bams", category: "required"}
+
+ # Optional parameters
+ unaccountedPath: {description: "The location to write reads to which are not detected as being part of an existing read group.", category: "common"}
+ filenameFormat: {description: "Format of the filename, the following tokens can be used: %% a literal % sign, %* basename, %# @RG index, %! @RG ID, %. filename extension for output format", category: "common"}
+ compressionLevel: {description: "Set compression level when writing gz or bgzf fastq files.", category: "advanced"}
+
+ # outputs
+ splitBam: {description: "BAM file split by read groups"}
+ splitBamIndex: {description: "BAM indexes"}
+ unaccounted: {description: "Reads with no RG tag or an unrecognised RG tag."}
}
}
task Tabix {
input {
File inputFile
- String outputFilePath = "indexed.vcf.gz"
- String type = "vcf"
- Int timeMinutes = 1 + ceil(size(inputFile, "G") * 2)
- String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
+ String outputFilePath = basename(inputFile)
+ String preset = "vcf"
+
+ Int timeMinutes = 1 + ceil(size(inputFile, "GiB") * 2)
+ String dockerImage = "quay.io/biocontainers/htslib:1.21--h566b1c6_1"
}
- # FIXME: It is better to do the indexing on VCF creation. Not in a separate task. With file localization this gets hairy fast.
+
+ # FIXME: It is better to do the indexing on VCF creation.
+ # Not in a separate task. With file localization this gets hairy fast.
command {
set -e
mkdir -p "$(dirname ~{outputFilePath})"
if [ ! -f ~{outputFilePath} ]
then
- ln ~{inputFile} ~{outputFilePath}
+ ln ~{inputFile} ~{outputFilePath} || cp ~{inputFile} ~{outputFilePath}
fi
- tabix ~{outputFilePath} -p ~{type}
+ tabix ~{outputFilePath} -p ~{preset}
}
output {
@@ -454,53 +681,64 @@ task Tabix {
}
runtime {
+ memory: "2GiB"
time_minutes: timeMinutes
- docker: dockerImage
+ docker: dockerImage
}
parameter_meta {
# inputs
inputFile: {description: "The file to be indexed.", category: "required"}
- outputFilePath: {description: "The location where the file should be written to. The index will appear alongside this link to the file.",
- category: "common"}
- type: {description: "The type of file (eg. vcf or bed) to be indexed.", category: "common"}
+ outputFilePath: {description: "The location where the file should be written to. The index will appear alongside this link to the file.", category: "common"}
+ preset: {description: "The preset for the file (eg. vcf or bed) to be indexed.", category: "common"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ indexedFile: {description: "Indexed input file."}
+ index: {description: "Index of the input file."}
}
}
task View {
input {
File inFile
- File? referenceFasta
String outputFileName = "view.bam"
Boolean uncompressedBamOutput = false
+
+ File? referenceFasta
Int? includeFilter
Int? excludeFilter
Int? excludeSpecificFilter
Int? MAPQthreshold
+ File? targetFile
+
+ Boolean fast = true # Sets compression level to 1.
Int threads = 1
- String memory = "1G"
- Int timeMinutes = 1 + ceil(size(inFile, "G") * 5)
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ String memory = "1GiB"
+ Int timeMinutes = 1 + ceil(size(inFile, "GiB") * 5)
+ String dockerImage = "quay.io/biocontainers/samtools:1.21--h96c455f_1"
}
+
String outputIndexPath = basename(outputFileName) + ".bai"
- # Always output to bam and output header
+ # Always output to bam and output header.
+ # -u should be after --fast, and will override it in that case.
command {
set -e
mkdir -p "$(dirname ~{outputFileName})"
samtools view -b \
~{"-T " + referenceFasta} \
~{"-o " + outputFileName} \
+ ~{true="--fast" false="" fast} \
~{true="-u " false="" uncompressedBamOutput} \
~{"-f " + includeFilter} \
~{"-F " + excludeFilter} \
~{"-G " + excludeSpecificFilter} \
~{"-q " + MAPQthreshold} \
- ~{"--threads " + (threads - 1)} \
+ --threads ~{threads - 1} \
+ ~{"--target-file " + targetFile} \
~{inFile}
samtools index ~{outputFileName} ~{outputIndexPath}
}
@@ -520,17 +758,22 @@ task View {
parameter_meta {
# inputs
inFile: {description: "A BAM, SAM or CRAM file.", category: "required"}
- referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
outputFileName: {description: "The location the output BAM file should be written.", category: "common"}
+ fast: {description: "Sets compression level to 1. Set to true by default.", category: "common"}
uncompressedBamOutput: {description: "Equivalent to samtools view's `-u` flag.", category: "advanced"}
+ referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
includeFilter: {description: "Equivalent to samtools view's `-f` option.", category: "advanced"}
excludeFilter: {description: "Equivalent to samtools view's `-F` option.", category: "advanced"}
excludeSpecificFilter: {description: "Equivalent to samtools view's `-G` option.", category: "advanced"}
MAPQthreshold: {description: "Equivalent to samtools view's `-q` option.", category: "advanced"}
+ targetFile: {description: "A BED file with regions to include", caegory: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: "Processed input file."}
+ outputBamIndex: {description: "Index of the processed input file."}
}
}
diff --git a/scripts b/scripts
index c0b48b0a..4142daab 160000
--- a/scripts
+++ b/scripts
@@ -1 +1 @@
-Subproject commit c0b48b0a916913d1e6751d7744d1cec37559a81f
+Subproject commit 4142daab81a7d9f28686b6a3299536757d381c81
diff --git a/seqtk.wdl b/seqtk.wdl
index 321ab132..f6fa422b 100644
--- a/seqtk.wdl
+++ b/seqtk.wdl
@@ -24,11 +24,12 @@ task Sample {
input {
File sequenceFile
String outFilePath = "subsampledReads.fq.gz"
- String? preCommand
- Int? seed
Boolean twoPassMode = false
- Float fractionOrNumber # when above 1.0 is the number of reads, otherwise it's a fraction
+ Float fractionOrNumber # When above 1.0 is the number of reads, otherwise it's a fraction.
Boolean zip = true
+
+ String? preCommand
+ Int? seed
}
command {
@@ -47,4 +48,4 @@ task Sample {
output {
File subsampledReads = outFilePath
}
-}
\ No newline at end of file
+}
diff --git a/sequali.wdl b/sequali.wdl
new file mode 100644
index 00000000..cbca3653
--- /dev/null
+++ b/sequali.wdl
@@ -0,0 +1,73 @@
+version 1.0
+
+# Copyright (c) 2024 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Sequali {
+ input {
+ File reads
+ File? mate_reads
+ String outDir = "."
+
+ Int threads = 2
+ String memory = "4GiB"
+ String dockerImage = "quay.io/biocontainers/sequali:0.12.0--py312hf67a6ed_0"
+ Int timeMinutes = 10 + ceil(size(reads, "GiB") + size(mate_reads, "GiB")) * 4
+ }
+
+ command <<<
+ set -e
+ mkdir -p $(dirname outputDir)
+ sequali \
+ --outdir ~{outDir} \
+ --threads ~{threads} \
+ ~{reads} \
+ ~{mate_reads}
+ >>>
+
+ output {
+ File html = outDir + "/" + basename(reads) + ".html"
+ File json = outDir + "/" + basename(reads) + ".json"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ docker: dockerImage
+ time_minutes: timeMinutes
+ }
+
+ parameter_meta {
+ # inputs
+ reads: {description: "A FASTQ or BAM file.", category: "required"}
+ mate_reads: {description: "FASTQ mate file"}
+ threads: {description: "The number of cores to use.", category: "advanced"}
+
+ outDir: {description: "The path to write the output to.", catgory: "required"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ html: {description: "HTML report file."}
+ json: {description: "JSON report file for use with MultiQC."}
+ }
+}
\ No newline at end of file
diff --git a/smoove.wdl b/smoove.wdl
index e8846f72..7a1ac38b 100644
--- a/smoove.wdl
+++ b/smoove.wdl
@@ -1,7 +1,5 @@
version 1.0
-# MIT License
-#
# Copyright (c) 2020 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -31,9 +29,9 @@ task Call {
String sample
String outputDir = "./smoove"
- String memory = "15G"
- String dockerImage = "quay.io/biocontainers/smoove:0.2.5--0"
+ String memory = "15GiB"
Int timeMinutes = 1440
+ String dockerImage = "quay.io/biocontainers/smoove:0.2.5--0"
}
command {
@@ -43,18 +41,19 @@ task Call {
--outdir ~{outputDir} \
--name ~{sample} \
--fasta ~{referenceFasta} \
+ --removepr \
+ --genotype \
~{bamFile}
}
output {
- File smooveVcf = outputDir + "/" + sample + "-smoove.vcf.gz"
+ File smooveVcf = outputDir + "/" + sample + "-smoove.genotyped.vcf.gz"
}
runtime {
memory: memory
- docker: dockerImage
time_minutes: timeMinutes
-
+ docker: dockerImage
}
parameter_meta {
@@ -63,10 +62,13 @@ task Call {
bamIndex: {description: "The index of the bam file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
- outputDir: {description: "The location the output VCF file should be written.", category: "common"}
sample: {description: "The name of the sample.", category: "required"}
+ outputDir: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum duration (in minutes) the tool is allowed to run.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ smooveVcf: {description: "Calls of structural variants in VCF file."}
}
}
diff --git a/snpeff.wdl b/snpeff.wdl
new file mode 100644
index 00000000..b972ab30
--- /dev/null
+++ b/snpeff.wdl
@@ -0,0 +1,111 @@
+version 1.0
+
+# MIT License
+#
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task SnpEff {
+ input {
+ File vcf
+ File vcfIndex
+ String genomeVersion
+ File datadirZip
+ String outputPath = "./snpeff.vcf"
+ Boolean hgvs = true
+ Boolean lof = true
+ Boolean noDownstream = false
+ Boolean noUpstream = false
+ Boolean noIntergenic = false
+ Boolean noShiftHgvs = false
+ Int? upDownStreamLen
+
+ String memory = "9GiB"
+ String javaXmx = "8G"
+ Int timeMinutes = 60
+ # Multicontainer with snpeff 5.2 and bgzip/tabix 1.19.1
+ String dockerImage = "quay.io/biocontainers/mulled-v2-2fe536b56916bd1d61a6a1889eb2987d9ea0cd2f:c51b2e46bf63786b2d9a7a7d23680791163ab39a-0"
+ }
+
+ Boolean compressed = basename(outputPath) != basename(outputPath, ".gz")
+
+ command {
+ set -e
+ ls ~{vcf} ~{vcfIndex} # dxCompiler localization workaroud
+ mkdir -p "$(dirname ~{outputPath})"
+ unzip ~{datadirZip}
+ snpEff -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -v \
+ ~{genomeVersion} \
+ -noDownload \
+ -dataDir $PWD/data \
+ ~{vcf} \
+ ~{true="-hgvs" false="-noHgvs" hgvs} \
+ ~{true="-lof" false="-noLof" lof} \
+ ~{true="-no-downstream" false="" noDownstream} \
+ ~{true="-no-upstream" false="" noUpstream} \
+ ~{true="-no-intergenic" false="" noIntergenic} \
+ ~{true="-noShiftHgvs" false="" noShiftHgvs} \
+ ~{"-upDownStreamLen " + upDownStreamLen} \
+ ~{if compressed then "| bgzip " else ""} > ~{outputPath}
+
+ ~{if compressed then "tabix ~{outputPath}" else ""}
+ rm -r $PWD/data
+ }
+
+ output {
+ File outputVcf = outputPath
+ File? outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ docker: dockerImage
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ memory: memory
+ }
+
+ parameter_meta {
+ # inputs
+ vcf: {description: "A VCF file to analyse.", category: "required"}
+ vcfIndex: {description: "The index for the VCF file.", category: "required"}
+ genomeVersion: {description: "The version of the genome to be used. The database for this genome must be present in the datadirZip.", category: "required"}
+ datadirZip: {description: "A zip file containing the directory of databases. This zip file must contain a directory called `data`, with the database mentioned in the genomeVersion input as subdirectory.",
+ category: "required"}
+ outputPath: {description: "The path to write the output to.", category: "common"}
+ hgvs: {description: "Equivalent to `-hgvs` if true or `-noHgvs` if false.", category: "advanced"}
+ lof: {description: "Equivalent to `-lof` if true or `-noLof` if false.", category: "advanced"}
+ noDownstream: {description: "Equivalent to the `-no-downstream` flag.", category: "advanced"}
+ noUpstream: {description: "Equivalent to the `-no-upstream` flag.", category: "advanced"}
+ noIntergenic: {description: "Equivalent to the `-no-intergenic` flag.", category: "advanced"}
+ noShiftHgvs: {description: "Equivalent to the `-noShiftHgvs` flag.", category: "advanced"}
+ upDownStreamLen: {descriptoin: "Equivalent to the `-upDownStreamLen` option.", category: "advanced"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "Annotated VCF file."}
+ outputVcfIndex: {description: "Index of annotated VCF file."}
+ }
+}
diff --git a/snpsift.wdl b/snpsift.wdl
new file mode 100644
index 00000000..a62f7295
--- /dev/null
+++ b/snpsift.wdl
@@ -0,0 +1,84 @@
+version 1.0
+
+# MIT License
+#
+# Copyright (c) 2025 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task SnpSiftFilter {
+ input {
+ File vcf
+ File? vcfIndex
+ String filterExpression
+ String outputPath = "./snpsift_filter.vcf"
+
+ String memory = "9GiB"
+ String javaXmx = "8G"
+ Int timeMinutes = 60
+ # Multicontainer with SnpSift 5.2 and bgzip/tabix 1.22
+ String dockerImage = "quay.io/biocontainers/mulled-v2-d4bc0c23eb1d95c7ecff7f0e8b3a4255503fd5d4:c51b2e46bf63786b2d9a7a7d23680791163ab39a-0"
+ }
+
+ Boolean compressed = basename(outputPath) != basename(outputPath, ".gz")
+
+ command {
+ set -e
+ ls ~{vcf} ~{vcfIndex} # dxCompiler localization workaroud
+
+ mkdir -p "$(dirname ~{outputPath})"
+ SnpSift -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ filter \
+ "~{filterExpression}" \
+ ~{vcf} \
+ ~{if compressed then "| bgzip " else ""} > ~{outputPath}
+
+ ~{if compressed then "tabix ~{outputPath}" else ""}
+ }
+
+ output {
+ File outputVcf = outputPath
+ File? outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ docker: dockerImage
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ memory: memory
+ }
+
+ parameter_meta {
+ # inputs
+ vcf: {description: "A VCF file to filter.", category: "required"}
+ vcfIndex: {description: "The index for the VCF file.", category: "common"}
+ filterExpression: {description: "The SnpSift filtering expression.", category: "required"}
+ outputPath: {description: "The path to write the output to.", category: "common"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "Filtered VCF file."}
+ outputVcfIndex: {description: "Index of filtered VCF file."}
+ }
+}
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 7b9a4403..7656d086 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -22,17 +22,18 @@ version 1.0
task ParallelPaired {
input {
- File? classifierSNV
- File? classifierIndel
String outputDir
File referenceFasta
File referenceFastaFai
- File? inclusionRegion
- File? exclusionRegion
File tumorBam
File tumorBamIndex
File normalBam
File normalBamIndex
+
+ File? classifierSNV
+ File? classifierIndel
+ File? inclusionRegion
+ File? exclusionRegion
File? mutect2VCF
File? varscanSNV
File? varscanIndel
@@ -46,6 +47,7 @@ task ParallelPaired {
File? strelkaSNV
File? strelkaIndel
+ String memory = "2GiB"
Int threads = 1
Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
@@ -90,22 +92,24 @@ task ParallelPaired {
runtime {
cpu: threads
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
- classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
+ # inputs
outputDir: {description: "The directory to write the output to.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
- exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
- normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
- normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
+ normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
+ normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
+ classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
+ classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
+ inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
+ exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanSNV: {description: "An SNV VCF as produced by varscan.", category: "advanced"}
varscanIndel: {description: "An indel VCF as produced by varscan.", category: "advanced"}
@@ -118,11 +122,16 @@ task ParallelPaired {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
-
threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ indels: {description: ""}
+ snvs: {description: ""}
+ ensembleIndels: {description: ""}
+ ensembleSNV: {description: ""}
}
}
@@ -133,12 +142,13 @@ task ParallelPairedTrain {
String outputDir
File referenceFasta
File referenceFastaFai
- File? inclusionRegion
- File? exclusionRegion
File tumorBam
File tumorBamIndex
File normalBam
File normalBamIndex
+
+ File? inclusionRegion
+ File? exclusionRegion
File? mutect2VCF
File? varscanSNV
File? varscanIndel
@@ -152,6 +162,7 @@ task ParallelPairedTrain {
File? strelkaSNV
File? strelkaIndel
+ String memory = "2GiB"
Int threads = 1
Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
@@ -195,22 +206,24 @@ task ParallelPairedTrain {
runtime {
cpu: threads
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
+ # inputs
truthSNV: {description: "A VCF of true SNVs.", category: "required"}
truthIndel: {description: "A VCF of true indels.", category: "required"}
outputDir: {description: "The directory to write the output to.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
- exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
- normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
- normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
+ normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
+ normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
+ inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
+ exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanSNV: {description: "An SNV VCF as produced by varscan.", category: "advanced"}
varscanIndel: {description: "An indel VCF as produced by varscan.", category: "advanced"}
@@ -223,25 +236,33 @@ task ParallelPairedTrain {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
-
threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ consensusIndels: {description: ""}
+ consensusSNV: {description: ""}
+ ensembleIndels: {description: ""}
+ ensembleSNV: {description: ""}
+ ensembleIndelsClassifier: {description: ""}
+ ensembleSNVClassifier: {description: ""}
}
}
task ParallelSingle {
input {
- File? classifierSNV
- File? classifierIndel
+ File bam
+ File bamIndex
String outputDir
File referenceFasta
File referenceFastaFai
+
+ File? classifierSNV
+ File? classifierIndel
File? inclusionRegion
File? exclusionRegion
- File bam
- File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
@@ -249,6 +270,7 @@ task ParallelSingle {
File? scalpelVCF
File? strelkaVCF
+ String memory = "2GiB"
Int threads = 1
Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
@@ -286,45 +308,53 @@ task ParallelSingle {
runtime {
cpu: threads
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
- classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
+ # inputs
+ bam: {description: "The input BAM file.", category: "required"}
+ bamIndex: {description: "The index for the input BAM file.", category: "required"}
outputDir: {description: "The directory to write the output to.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
+ classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
- bam: {description: "The input BAM file.", category: "required"}
- bamIndex: {description: "The index for the input BAM file.", category: "required"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanVCF: {description: "A VCF as produced by varscan.", category: "advanced"}
vardictVCF: {description: "A VCF as produced by vardict.", category: "advanced"}
lofreqVCF: {description: "A VCF as produced by lofreq.", category: "advanced"}
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
-
threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ indels: {description: ""}
+ snvs: {description: ""}
+ ensembleIndels: {description: ""}
+ ensembleSNV: {description: ""}
}
}
task ParallelSingleTrain {
input {
+ File bam
+ File bamIndex
File truthSNV
File truthIndel
String outputDir
File referenceFasta
File referenceFastaFai
+
File? inclusionRegion
File? exclusionRegion
- File bam
- File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
@@ -332,6 +362,7 @@ task ParallelSingleTrain {
File? scalpelVCF
File? strelkaVCF
+ String memory = "2GiB"
Int threads = 1
Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
@@ -368,11 +399,15 @@ task ParallelSingleTrain {
runtime {
cpu: threads
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
+ # inputs
+ bam: {description: "The input BAM file.", category: "required"}
+ bamIndex: {description: "The index for the input BAM file.", category: "required"}
truthSNV: {description: "A VCF of true SNVs.", category: "required"}
truthIndel: {description: "A VCF of true indels.", category: "required"}
outputDir: {description: "The directory to write the output to.", category: "common"}
@@ -380,19 +415,24 @@ task ParallelSingleTrain {
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
- bam: {description: "The input BAM file.", category: "required"}
- bamIndex: {description: "The index for the input BAM file.", category: "required"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanVCF: {description: "A VCF as produced by varscan.", category: "advanced"}
vardictVCF: {description: "A VCF as produced by vardict.", category: "advanced"}
lofreqVCF: {description: "A VCF as produced by lofreq.", category: "advanced"}
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
-
threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ consensusIndels: {description: ""}
+ consensusSNV: {description: ""}
+ ensembleIndels: {description: ""}
+ ensembleSNV: {description: ""}
+ ensembleIndelsClassifier: {description: ""}
+ ensembleSNVClassifier: {description: ""}
}
}
@@ -400,17 +440,17 @@ task ModifyStrelka {
input {
File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz")
- String dockerImage = "lethalfang/somaticseq:3.1.0"
+
+ String memory = "2GiB"
Int timeMinutes = 20
+ String dockerImage = "lethalfang/somaticseq:3.1.0"
}
command {
set -e
-
/opt/somaticseq/vcfModifier/modify_Strelka.py \
-infile ~{strelkaVCF} \
-outfile "modified_strelka.vcf"
-
first_FORMAT_line_num=$(grep -n -m 1 '##FORMAT' "modified_strelka.vcf" | cut -d : -f 1)
sed "$first_FORMAT_line_num"'i##FORMAT=' "modified_strelka.vcf" > ~{outputVCFName}
}
@@ -420,15 +460,20 @@ task ModifyStrelka {
}
runtime {
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
+ # inputs
strelkaVCF: {description: "A vcf file as produced by strelka.", category: "required"}
outputVCFName: {description: "The location the output VCF file should be written to.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: ""}
}
}
diff --git a/spades.wdl b/spades.wdl
index 204dbfea..d717ab28 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -22,10 +22,11 @@ version 1.0
task Spades {
input {
- String outputDir
- String? preCommand
File read1
File? read2
+ String outputDir
+
+ String? preCommand
File? interlacedReads
File? sangerReads
File? pacbioReads
@@ -33,23 +34,24 @@ task Spades {
File? tslrContigs
File? trustedContigs
File? untrustedContigs
- Boolean? singleCell
- Boolean? metagenomic
- Boolean? rna
- Boolean? plasmid
- Boolean? ionTorrent
- Boolean? onlyErrorCorrection
- Boolean? onlyAssembler
- Boolean? careful
- Boolean? disableGzipOutput
- Boolean? disableRepeatResolution
+ Boolean singleCell = false
+ Boolean metagenomic = false
+ Boolean rna = false
+ Boolean plasmid = false
+ Boolean ionTorrent = false
+ Boolean onlyErrorCorrection = false
+ Boolean onlyAssembler = false
+ Boolean careful = false
+ Boolean disableGzipOutput = false
+ Boolean disableRepeatResolution = false
File? dataset
- Int threads = 1
- Int memoryGb = 16
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
+
+ Int threads = 1
+ Int memoryGb = 16
}
command {
@@ -98,6 +100,6 @@ task Spades {
runtime {
cpu: threads
- memory: "~{memoryGb}G"
+ memory: "~{memoryGb}GiB"
}
-}
\ No newline at end of file
+}
diff --git a/star.wdl b/star.wdl
index 3d0e2eb0..88d3c838 100644
--- a/star.wdl
+++ b/star.wdl
@@ -24,12 +24,13 @@ task GenomeGenerate {
input {
String genomeDir = "STAR_index"
File referenceFasta
+
File? referenceGtf
Int? sjdbOverhang
Int threads = 4
- String memory = "32G"
- Int timeMinutes = ceil(size(referenceFasta, "G") * 240 / threads)
+ String memory = "32GiB"
+ Int timeMinutes = ceil(size(referenceFasta, "GiB") * 240 / threads)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
}
@@ -61,8 +62,10 @@ task GenomeGenerate {
File? sjdbListFromGtfOut = "~{genomeDir}/sjdbList.fromGTF.out.tab"
File? sjdbListOut = "~{genomeDir}/sjdbList.out.tab"
File? transcriptInfo = "~{genomeDir}/transcriptInfo.tab"
- Array[File] starIndex = select_all([chrLength, chrNameLength, chrName, chrStart, genome, genomeParameters,
- sa, saIndex, exonGeTrInfo, exonInfo, geneInfo, sjdbInfo, sjdbListFromGtfOut,
+ Array[File] starIndex = select_all([chrLength, chrNameLength, chrName,
+ chrStart, genome, genomeParameters,
+ sa, saIndex, exonGeTrInfo, exonInfo,
+ geneInfo, sjdbInfo, sjdbListFromGtfOut,
sjdbListOut, transcriptInfo])
}
@@ -74,16 +77,33 @@ task GenomeGenerate {
}
parameter_meta {
- genomeDir: {description:"The directory the STAR index should be written to.", categroy: "common"}
+ # inputs
+ genomeDir: {description:"The directory the STAR index should be written to.", category: "common"}
referenceFasta: {description: "The reference Fasta file.", category: "required"}
referenceGtf: {description: "The reference GTF file.", category: "common"}
sjdbOverhang: {description: "Equivalent to STAR's `--sjdbOverhang` option.", category: "advanced"}
-
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ chrLength: {description: "Text chromosome lengths file."}
+ chrNameLength: {description: "Text chromosome name lengths file."}
+ chrName: {description: "Text chromosome names file."}
+ chrStart: {description: "Chromosome start sites file."}
+ genome: {description: "Binary genome sequence file."}
+ genomeParameters: {description: "Genome parameters file."}
+ sa: {description: "Suffix arrays file."}
+ saIndex: {description: "Index file of suffix arrays."}
+ exonGeTrInfo: {description: "Exon, gene and transcript information file."}
+ exonInfo: {description: "Exon information file."}
+ geneInfo: {description: "Gene information file."}
+ sjdbInfo: {description: "Splice junctions coordinates file."}
+ sjdbListFromGtfOut: {description: "Splice junctions from input GTF file."}
+ sjdbListOut: {description: "Splice junction list file."}
+ transcriptInfo: {description: "Transcripts information file."}
+ starIndex: {description: "A collection of all STAR index files."}
}
}
@@ -95,6 +115,8 @@ task Star {
String outFileNamePrefix
String outSAMtype = "BAM SortedByCoordinate"
String readFilesCommand = "zcat"
+ Int outBAMcompression = 1
+
Int? outFilterScoreMin
Float? outFilterScoreMinOverLread
Int? outFilterMatchNmin
@@ -103,23 +125,22 @@ task Star {
String? twopassMode = "Basic"
Array[String]? outSAMattrRGline
String? outSAMunmapped = "Within KeepPairs"
- Int outBAMcompression = 1
Int? limitBAMsortRAM
Int runThreadN = 4
String? memory
# 1 minute initialization + time reading in index (1 minute per G) + time aligning data.
- Int timeMinutes = 1 + ceil(size(indexFiles, "G")) + ceil(size(flatten([inputR1, inputR2]), "G") * 300 / runThreadN)
+ Int timeMinutes = 1 + ceil(size(indexFiles, "GiB")) + ceil(size(flatten([inputR1, inputR2]), "GiB") * 300 / runThreadN)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
}
# Use a margin of 30% index size. Real memory usage is ~30 GiB for a 27 GiB index.
- Int memoryGb = 1 + ceil(size(indexFiles, "G") * 1.3)
+ Int memoryGb = 1 + ceil(size(indexFiles, "GiB") * 1.3)
# For some reason doing above calculation inside a string does not work.
# So we solve it with an optional memory string and using select_first
# in the runtime section.
- #TODO Could be extended for all possible output extensions
+ #TODO: Could be extended for all possible output extensions.
Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
command {
@@ -151,18 +172,20 @@ task Star {
runtime {
cpu: runThreadN
- memory: select_first([memory, "~{memoryGb}G"])
+ memory: select_first([memory, "~{memoryGb}GiB"])
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
+ # inputs
inputR1: {description: "The first-/single-end FastQ files.", category: "required"}
inputR2: {description: "The second-end FastQ files (in the same order as the first-end files).", category: "common"}
indexFiles: {description: "The star index files.", category: "required"}
outFileNamePrefix: {description: "The prefix for the output files. May include directories.", category: "required"}
outSAMtype: {description: "The type of alignment file to be produced. Currently only `BAM SortedByCoordinate` is supported.", category: "advanced"}
readFilesCommand: {description: "Equivalent to star's `--readFilesCommand` option.", category: "advanced"}
+ outBAMcompression: {description: "The compression level of the output BAM.", category: "advanced"}
outFilterScoreMin: {description: "Equivalent to star's `--outFilterScoreMin` option.", category: "advanced"}
outFilterScoreMinOverLread: {description: "Equivalent to star's `--outFilterScoreMinOverLread` option.", category: "advanced"}
outFilterMatchNmin: {description: "Equivalent to star's `--outFilterMatchNmin` option.", category: "advanced"}
@@ -174,9 +197,12 @@ task Star {
limitBAMsortRAM: {description: "Equivalent to star's `--limitBAMsortRAM` option.", category: "advanced"}
runThreadN: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- outBAMcompression: {description: "The compression level of the output BAM.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ bamFile: {description: "Alignment file."}
+ logFinalOut: {description: "Log information file."}
}
}
diff --git a/strelka.wdl b/strelka.wdl
index 50c38b55..39afe172 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -29,11 +29,12 @@ task Germline {
Array[File]+ indexes
File referenceFasta
File referenceFastaFai
- File? callRegions
- File? callRegionsIndex
Boolean exome = false
Boolean rna = false
+ File? callRegions
+ File? callRegionsIndex
+
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 90
@@ -61,28 +62,31 @@ task Germline {
}
runtime {
- docker: dockerImage
cpu: cores
+ memory: "~{memoryGb}GiB"
time_minutes: timeMinutes
- memory: "~{memoryGb}G"
+ docker: dockerImage
}
parameter_meta {
+ # inputs
runDir: {description: "The directory to use as run/output directory.", category: "common"}
bams: {description: "The input BAM files.", category: "required"}
indexes: {description: "The indexes for the input BAM files.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
- callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
rna: {description: "Whether or not the data is from RNA sequencing.", category: "common"}
-
+ callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
+ callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ variants: {description: "Output VCF file."}
+ variantsIndex: {description: "Index of output VCF file."}
}
}
@@ -95,11 +99,12 @@ task Somatic {
File tumorBamIndex
File referenceFasta
File referenceFastaFai
+ Boolean exome = false
+
File? callRegions
File? callRegionsIndex
File? indelCandidatesVcf
File? indelCandidatesVcfIndex
- Boolean exome = false
Int cores = 1
Int memoryGb = 4
@@ -133,13 +138,14 @@ task Somatic {
}
runtime {
- docker: dockerImage
cpu: cores
+ memory: "~{memoryGb}GiB"
time_minutes: timeMinutes
- memory: "~{memoryGb}G"
+ docker: dockerImage
}
parameter_meta {
+ # inputs
runDir: {description: "The directory to use as run/output directory.", category: "common"}
normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
@@ -147,17 +153,21 @@ task Somatic {
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
indelCandidatesVcf: {description: "An indel candidates VCF file from manta.", category: "advanced"}
indelCandidatesVcfIndex: {description: "The index for the indel candidates VCF file.", category: "advanced"}
- exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
-
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ indelsVcf: {description: "VCF containing INDELS."}
+ indelsIndex: {description: "Index of output `indelsVcf`."}
+ variants: {description: "VCF containing variants."}
+ variantsIndex: {description: "Index of output `variants`."}
}
meta {
@@ -165,4 +175,4 @@ task Somatic {
exclude: ["doNotDefineThis"]
}
}
-}
\ No newline at end of file
+}
diff --git a/stringtie.wdl b/stringtie.wdl
index 5ed62dea..fbe7e442 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -24,17 +24,19 @@ task Stringtie {
input {
File bam
File bamIndex
- File? referenceGtf
Boolean skipNovelTranscripts = false
String assembledTranscriptsFile
+
+ File? referenceGtf
Boolean? firstStranded
Boolean? secondStranded
String? geneAbundanceFile
+ Float? minimumCoverage
Int threads = 1
- String memory = "2G"
+ String memory = "2GiB"
Int timeMinutes = 1 + ceil(size(bam, "G") * 60 / threads)
- String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
+ String dockerImage = "quay.io/biocontainers/stringtie:1.3.6--h92e31bf_0"
}
command {
@@ -46,6 +48,7 @@ task Stringtie {
~{true="-e" false="" skipNovelTranscripts} \
~{true="--rf" false="" firstStranded} \
~{true="--fr" false="" secondStranded} \
+ ~{"-c " + minimumCoverage} \
-o ~{assembledTranscriptsFile} \
~{"-A " + geneAbundanceFile} \
~{bam}
@@ -64,19 +67,24 @@ task Stringtie {
}
parameter_meta {
+ # inputs
bam: {description: "The input BAM file.", category: "required"}
bamIndex: {description: "The input BAM file's index.", category: "required"}
- referenceGtf: {description: "A reference GTF file to be used as guide.", category: "common"}
skipNovelTranscripts: {description: "Whether new transcripts should be assembled or not.", category: "common"}
assembledTranscriptsFile: {description: "Where the output of the assembly should be written.", category: "required"}
+ referenceGtf: {description: "A reference GTF file to be used as guide.", category: "common"}
firstStranded: {description: "Equivalent to the --rf flag of stringtie.", category: "required"}
secondStranded: {description: "Equivalent to the --fr flag of stringtie.", category: "required"}
geneAbundanceFile: {description: "Where the abundance file should be written.", category: "common"}
+ minimumCoverage: {description: "The minimum coverage for a transcript to be shown in the output.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ assembledTranscripts: {description: "GTF file containing the assembled transcripts."}
+ geneAbundance: {description: "Gene abundances in tab-delimited format."}
}
}
@@ -84,18 +92,19 @@ task Merge {
input {
Array[File]+ gtfFiles
String outputGtfPath
+ Boolean keepMergedTranscriptsWithRetainedIntrons = false
+
File? guideGtf
Int? minimumLength
Float? minimumCoverage
Float? minimumFPKM
Float? minimumTPM
Float? minimumIsoformFraction
- Boolean keepMergedTranscriptsWithRetainedIntrons = false
String? label
- String memory = "10G"
+ String memory = "10GiB"
Int timeMinutes = 1 + ceil(size(gtfFiles, "G") * 20)
- String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
+ String dockerImage = "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
}
command {
@@ -125,19 +134,22 @@ task Merge {
}
parameter_meta {
+ # inputs
gtfFiles: {description: "The GTF files produced by stringtie.", category: "required"}
outputGtfPath: {description: "Where the output should be written.", category: "required"}
+ keepMergedTranscriptsWithRetainedIntrons: {description: "Equivalent to the -i flag of 'stringtie --merge'.", category: "advanced"}
guideGtf: {description: "Equivalent to the -G option of 'stringtie --merge'.", category: "advanced"}
minimumLength: {description: "Equivalent to the -m option of 'stringtie --merge'.", category: "advanced"}
minimumCoverage: {description: "Equivalent to the -c option of 'stringtie --merge'.", category: "advanced"}
minimumFPKM: {description: "Equivalent to the -F option of 'stringtie --merge'.", category: "advanced"}
minimumTPM: {description: "Equivalent to the -T option of 'stringtie --merge'.", category: "advanced"}
minimumIsoformFraction: {description: "Equivalent to the -f option of 'stringtie --merge'.", category: "advanced"}
- keepMergedTranscriptsWithRetainedIntrons: {description: "Equivalent to the -i flag of 'stringtie --merge'.", category: "advanced"}
label: {description: "Equivalent to the -l option of 'stringtie --merge'.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ mergedGtfFile: {description: "A merged GTF file from a set of GTF files."}
}
}
diff --git a/survivor.wdl b/survivor.wdl
index e5ac7b5b..ae246f60 100644
--- a/survivor.wdl
+++ b/survivor.wdl
@@ -1,7 +1,5 @@
version 1.0
-# MIT License
-#
# Copyright (c) 2018 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -27,14 +25,15 @@ task Merge {
Array[File] filePaths
Int breakpointDistance = 1000
Int suppVecs = 2
- Int svType = 1
- Int strandType = 1
- Int distanceBySvSize = 0
+ Boolean svType = true
+ Boolean strandType = true
+ Boolean distanceBySvSize = false
Int minSize = 30
String outputPath = "./survivor/merged.vcf"
- String memory = "24G"
+
+ String memory = "24GiB"
Int timeMinutes = 60
- String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
+ String dockerImage = "quay.io/biocontainers/survivor:1.0.7--hd03093a_2"
}
command {
@@ -45,9 +44,9 @@ task Merge {
fileList \
~{breakpointDistance} \
~{suppVecs} \
- ~{svType} \
- ~{strandType} \
- ~{distanceBySvSize} \
+ ~{true='1' false='0' svType} \
+ ~{true='1' false='0' strandType} \
+ ~{true='1' false='0' distanceBySvSize} \
~{minSize} \
~{outputPath}
}
@@ -64,16 +63,19 @@ task Merge {
parameter_meta {
# inputs
- filePaths: {description: "An array of VCF files (predictions) to be merged by SURVIVOR", category: "required"}
- breakpointDistance: {description: "The distance between pairwise breakpoints between SVs", category: "advanced"}
- suppVecs: {description: "The minimum number of SV callers to support the merging", category: "advanced"}
- svType: {description: "A boolean to include the type SV to be merged", category: "advanced"}
- strandType: {description: "A boolean to include strand type of an SV to be merged", category: "advanced"}
- distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "advanced"}
- minSize: {description: "The mimimum size of SV to be merged", category: "advanced"}
+ filePaths: {description: "An array of VCF files (predictions) to be merged by SURVIVOR.", category: "required"}
+ breakpointDistance: {description: "The distance between pairwise breakpoints between SVs.", category: "advanced"}
+ suppVecs: {description: "The minimum number of SV callers to support the merging.", category: "advanced"}
+ svType: {description: "A boolean to include the type SV to be merged.", category: "advanced"}
+ strandType: {description: "A boolean to include strand type of an SV to be merged.", category: "advanced"}
+ distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size.", category: "advanced"}
+ minSize: {description: "The mimimum size of SV to be merged.", category: "advanced"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
- memory: {description: "The memory required to run the programs", category: "advanced"}
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ mergedVcf: {description: "All the vcf files specified in fileList merged."}
}
}
diff --git a/talon.wdl b/talon.wdl
index c11ab9e0..2f93e36b 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+# Copyright (c) 2019 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -30,7 +30,7 @@ task CreateAbundanceFileFromDatabase {
File? whitelistFile
File? datasetsFile
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -86,7 +86,7 @@ task CreateGtfFromDatabase {
File? whitelistFile
File? datasetFile
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -144,7 +144,7 @@ task FilterTalonTranscripts {
File? datasetsFile
Int? minDatasets
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -200,7 +200,7 @@ task GetReadAnnotations {
File? datasetFile
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -248,7 +248,7 @@ task GetSpliceJunctions {
String runMode = "intron"
String outputPrefix
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -302,7 +302,7 @@ task InitializeTalonDatabase {
Int cutOff3p = 300
String outputPrefix
- String memory = "10G"
+ String memory = "10GiB"
Int timeMinutes = 60
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -360,7 +360,7 @@ task LabelReads {
String outputPrefix
Int threads = 4
- String memory = "25G"
+ String memory = "25GiB"
Int timeMinutes = 2880
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -413,7 +413,7 @@ task ReformatGtf {
input {
File gtfFile
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -454,7 +454,7 @@ task SummarizeDatasets {
File? datasetGroupsCsv
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 50
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
@@ -506,7 +506,7 @@ task Talon {
String outputPrefix
Int threads = 4
- String memory = "25G"
+ String memory = "25GiB"
Int timeMinutes = 2880
String dockerImage = "biocontainers/talon:v5.0_cv1"
}
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index 79661307..8607a7a3 100644
--- a/transcriptclean.wdl
+++ b/transcriptclean.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+# Copyright (c) 2019 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -27,7 +27,7 @@ task GetSJsFromGtf {
String outputPrefix
Int minIntronSize = 21
- String memory = "8G"
+ String memory = "8GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
@@ -54,10 +54,10 @@ task GetSJsFromGtf {
parameter_meta {
# inputs
- gtfFile: {description: "Input gtf file", category: "required"}
- genomeFile: {description: "Reference genome", category: "required"}
- minIntronSize: {description: "Minimum size of intron to consider a junction.", category: "advanced"}
+ gtfFile: {description: "Input gtf file.", category: "required"}
+ genomeFile: {description: "Reference genome.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ minIntronSize: {description: "Minimum size of intron to consider a junction.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
@@ -72,7 +72,7 @@ task GetTranscriptCleanStats {
File inputSam
String outputPrefix
- String memory = "4G"
+ String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
@@ -97,7 +97,7 @@ task GetTranscriptCleanStats {
parameter_meta {
# inputs
- inputSam: {description: "Output sam file from transcriptclean", category: "required"}
+ inputSam: {description: "Output sam file from transcriptclean.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
@@ -128,7 +128,7 @@ task TranscriptClean {
File? variantFile
Int cores = 1
- String memory = "25G"
+ String memory = "25GiB"
Int timeMinutes = 2880
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
@@ -189,8 +189,7 @@ task TranscriptClean {
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
fastaFile: {description: "Fasta file containing corrected reads."}
diff --git a/umi-tools.wdl b/umi-tools.wdl
index c5f3b145..d8d17c48 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2017 Sequencing Analysis Support Core - Leiden University Medical Center
+# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -26,11 +26,13 @@ task Extract {
File? read2
String bcPattern
String? bcPattern2
- Boolean threePrime = false
String read1Output = "umi_extracted_R1.fastq.gz"
String? read2Output = "umi_extracted_R2.fastq.gz"
+ Boolean threePrime = false
+
+ String memory = "20GiB"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
- String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
+ String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
}
command {
@@ -50,21 +52,26 @@ task Extract {
}
runtime {
- docker: dockerImage
+ memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
read1: {description: "The first/single-end fastq file.", category: "required"}
read2: {description: "The second-end fastq file.", category: "common"}
bcPattern: {description: "The pattern to be used for UMI extraction. See the umi_tools docs for more information.", category: "required"}
bcPattern2: {description: "The pattern to be used for UMI extraction in the second-end reads. See the umi_tools docs for more information.", category: "advanced"}
- threePrime: {description: "Whether or not the UMI's are at the reads' 3' end. If false the UMIs are extracted from the 5' end.", category: "advanced"}
read1Output: {description: "The location to write the first/single-end output fastq file to.", category: "advanced"}
read2Output: {description: "The location to write the second-end output fastq file to.", category: "advanced"}
+ threePrime: {description: "Whether or not the UMI's are at the reads' 3' end. If false the UMIs are extracted from the 5' end.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ extractedRead1: {description: "First read with UMI extracted to read name."}
+ extractedRead2: {description: "Second read with UMI extracted to read name."}
}
}
@@ -72,29 +79,31 @@ task Dedup {
input {
File inputBam
File inputBamIndex
- String? umiSeparator
String outputBamPath
- String? statsPrefix
+ String tmpDir = "./umiToolsDedupTmpDir"
+
Boolean paired = true
- String memory = "25G"
- Int timeMinutes = 30 + ceil(size(inputBam, "G") * 30)
+ String? umiSeparator
+ String? statsPrefix
- # Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9)
- String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
+ String memory = "25GiB"
+ Int timeMinutes = 30 + ceil(size(inputBam, "GiB") * 30)
+ String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
}
String outputBamIndex = sub(outputBamPath, "\.bam$", ".bai")
command {
set -e
- mkdir -p "$(dirname ~{outputBamPath})"
+ mkdir -p "$(dirname ~{outputBamPath})" "~{tmpDir}"
umi_tools dedup \
- --stdin ~{inputBam} \
- --stdout ~{outputBamPath} \
+ --stdin=~{inputBam} \
+ --stdout=~{outputBamPath} \
~{"--output-stats " + statsPrefix} \
~{"--umi-separator=" + umiSeparator} \
- ~{true="--paired" false="" paired}
+ ~{true="--paired" false="" paired} \
+ --temp-dir=~{tmpDir}
samtools index ~{outputBamPath} ~{outputBamIndex}
}
@@ -107,21 +116,29 @@ task Dedup {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBam: {description: "The input BAM file.", categrory: "required"}
inputBamIndex: {description: "The index for the ipnut BAM file.", cateogry: "required"}
outputBamPath: {description: "The location to write the output BAM file to.", category: "required"}
- statsPrefix: {description: "The prefix for the stats files.", category: "advanced"}
- umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
+ tmpDir: {description: "Temporary directory.", category: "advanced"}
paired: {description: "Whether or not the data is paired.", category: "common"}
+ umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
+ statsPrefix: {description: "The prefix for the stats files.", category: "advanced"}
memory: {description: "The amount of memory required for the task.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ deduppedBam: {description: "Deduplicated BAM file."}
+ deduppedBamIndex: {description: "Index of the deduplicated BAM file."}
+ editDistance: {description: "Report of the (binned) average edit distance between the UMIs at each position."}
+ umiStats: {description: "UMI-level summary statistics."}
+ positionStats: {description: "The counts for unique combinations of UMI and position."}
}
}
diff --git a/umi.wdl b/umi.wdl
new file mode 100644
index 00000000..0628783a
--- /dev/null
+++ b/umi.wdl
@@ -0,0 +1,107 @@
+version 1.0
+
+# Copyright (c) 2022 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task BamReadNameToUmiTag {
+
+ # This task processes a bam file with reads that have been extracted with
+ # umi-tools extract. The UMI is extracted from the read name again and put
+ # in the bam file again with umiTag (default RX)
+ input {
+ File inputBam
+ String outputPath = "output.bam"
+ String umiTag = "RX"
+ String separatorChar = "_"
+
+ String memory = "2GiB"
+ Int timeMinutes = 1 + ceil(size([inputBam], "GiB") * 10)
+ String dockerImage = "quay.io/biocontainers/pysam:0.17.0--py39h051187c_0"
+ }
+
+ String bamIndexPath = sub(select_first([outputPath]), "\.bam$", ".bai")
+
+ command <<<
+ python < Tuple[str, str]:
+ id_and_rest = name.split(maxsplit=1)
+ id = id_and_rest[0]
+ # If there was no whitespace id_and_rest will have length 1
+ other_parts = id_and_rest[1] if len(id_and_rest) == 2 else ""
+ underscore_index = id.rfind(separator_char)
+ umi = id[underscore_index + 1:]
+ new_id = id[:underscore_index]
+ if other_parts:
+ return " ".join([new_id, other_parts]), umi
+ return new_id, umi
+
+ def annotate_umis(in_file, out_file, bam_tag="RX", separator_char = "_"):
+ in_bam = pysam.AlignmentFile(in_file, "rb")
+ os.makedirs(os.path.dirname(out_file), exist_ok=True)
+ out_bam = pysam.AlignmentFile(out_file, "wb", template=in_bam)
+ # Encode bam_tag as bytes. Otherwise pysam converts it to bytes anyway.
+ encoded_bam_tag = bam_tag.encode('ascii')
+ for segment in in_bam: # type: pysam.AlignedSegment
+ new_name, umi = split_umi_from_name(segment.query_name, separator_char)
+ segment.query_name = new_name
+ # Encode umi as ascii. Otherwise pysam encodes it to bytes anyway.
+ # Value type has to be a string though, otherwise pysam crashes.
+ segment.set_tag(encoded_bam_tag, umi.encode('ascii'), value_type="Z")
+ out_bam.write(segment)
+
+ if __name__ == "__main__":
+ annotate_umis("~{inputBam}", "~{outputPath}", "~{umiTag}", "~{separatorChar}")
+ pysam.index("~{outputPath}", "~{bamIndexPath}", b=True)
+ CODE
+ >>>
+
+ output {
+ File outputBam = outputPath
+ File outputBamIndex = bamIndexPath
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputBam: {description: "The input SAM file.", category: "required"}
+ outputPath: {description: "Output directory path + output file.", category: "common"}
+ umiTag: {description: "The tag used for UMIs in the output BAM file.", category: "common"}
+ separatorChar: {description: "Character used to separate the UMIs from the read name.", category: "common"}
+
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputBam: {description: "Sorted BAM file."}
+ outputBamIndex: {description: "Sorted BAM file index."}
+ }
+}
diff --git a/unicycler.wdl b/unicycler.wdl
index fc393603..d83db3ca 100644
--- a/unicycler.wdl
+++ b/unicycler.wdl
@@ -22,12 +22,13 @@ version 1.0
task Unicycler {
input {
+ String out
+
String? preCommand
File? short1
File? short2
File? unpaired
File? long
- String out
Int? verbosity
Int? minFastaLength
Int? keep
@@ -65,7 +66,7 @@ task Unicycler {
String? lowScore
Int threads = 1
- String memory = "4G"
+ String memory = "4GiB"
}
command {
@@ -125,4 +126,4 @@ task Unicycler {
cpu: threads
memory: memory
}
-}
\ No newline at end of file
+}
diff --git a/vardict.wdl b/vardict.wdl
index 92beb32e..187b4567 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -27,29 +27,28 @@ task VarDict {
String tumorSampleName
File tumorBam
File tumorBamIndex
- String? normalSampleName
- File? normalBam
- File? normalBamIndex
File referenceFasta
File referenceFastaFai
File bedFile
String outputVcf
-
- Int chromosomeColumn = 1
- Int startColumn = 2
- Int endColumn = 3
- Int geneColumn = 4
-
Boolean outputCandidateSomaticOnly = true
Boolean outputAllVariantsAtSamePosition = true
Float mappingQuality = 20
Int minimumTotalDepth = 8
Int minimumVariantDepth = 4
Float minimumAlleleFrequency = 0.02
+ Int chromosomeColumn = 1
+ Int startColumn = 2
+ Int endColumn = 3
+ Int geneColumn = 4
+
+ String? normalSampleName
+ File? normalBam
+ File? normalBamIndex
- Int threads = 1
- String memory = "18G"
String javaXmx = "16G"
+ Int threads = 1
+ String memory = "18GiB"
Int timeMinutes = 300
String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
}
@@ -93,33 +92,34 @@ task VarDict {
}
parameter_meta {
+ # inputs
tumorSampleName: {description: "The name of the tumor/case sample.", category: "required"}
tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
- normalSampleName: {description: "The name of the normal/control sample.", category: "common"}
- normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
- normalBamIndex: {description: "The normal/control sample's BAM file.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
bedFile: {description: "A bed file describing the regions to operate on. These regions must be below 1e6 bases in size.", category: "required"}
outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
- chromosomeColumn: {description: "Equivalent to vardict-java's `-c` option.", category: "advanced"}
- startColumn: {description: "Equivalent to vardict-java's `-S` option.", category: "advanced"}
- endColumn: {description: "Equivalent to vardict-java's `-E` option.", category: "advanced"}
- geneColumn: {description: "Equivalent to vardict-java's `-g` option.", category: "advanced"}
outputCandidateSomaticOnly: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-M` flag.", category: "advanced"}
outputAllVariantsAtSamePosition: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-A` flag.", category: "advanced"}
mappingQuality: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-Q` option.", category: "advanced"}
minimumTotalDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-d` option.", category: "advanced"}
minimumVariantDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-v` option.", category: "advanced"}
minimumAlleleFrequency: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-f` option.", category: "advanced"}
-
+ chromosomeColumn: {description: "Equivalent to vardict-java's `-c` option.", category: "advanced"}
+ startColumn: {description: "Equivalent to vardict-java's `-S` option.", category: "advanced"}
+ endColumn: {description: "Equivalent to vardict-java's `-E` option.", category: "advanced"}
+ geneColumn: {description: "Equivalent to vardict-java's `-g` option.", category: "advanced"}
+ normalSampleName: {description: "The name of the normal/control sample.", category: "common"}
+ normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
+ normalBamIndex: {description: "The normal/control sample's BAM file.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ vcfFile: {description: "Output VCF file."}
}
}
diff --git a/vep.wdl b/vep.wdl
new file mode 100644
index 00000000..2c1f923b
--- /dev/null
+++ b/vep.wdl
@@ -0,0 +1,110 @@
+version 1.0
+
+# Copyright (c) 2017 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Vep {
+ input {
+ File inputFile
+ String outputPath = "vep.annotated.vcf.gz"
+ File cacheTar
+ File? pluginsTar
+ String? species
+ Array[String] plugins = []
+ Boolean refseq = false
+ Boolean merged = false
+
+ Boolean everything = false
+ Boolean symbol = false
+
+ String memory = "8GiB"
+ # Account time for unpacking the cache.
+ Int timeMinutes = 1 + ceil(size(cacheTar, "GiB")) + ceil(size(inputFile, "MiB") * 15)
+ String dockerImage = "quay.io/biocontainers/ensembl-vep:113.3--pl5321h2a3209d_0"
+ }
+
+ command <<<
+ set -eu
+ mkdir vep_cache
+ mkdir -p "$(dirname ~{outputPath})"
+ tar -x --directory vep_cache -f ~{cacheTar}
+ ~{"tar -x --directory vep_cache -f " + pluginsTar}
+
+ # Make sure vep can error, so the removal always succeeds.
+ set +e
+ # Output all stats files by default for MultiQC integration
+ vep \
+ --input_file ~{inputFile} \
+ --output_file ~{outputPath} \
+ ~{"--species " + species} \
+ --stats_html --stats_text \
+ --dir vep_cache \
+ --offline \
+ ~{true="--plugin" false="" length(plugins) > 0} ~{sep=" --plugin " plugins} \
+ --vcf \
+ --compress_output bgzip \
+ ~{true="--refseq" false="" refseq} \
+ ~{true="--merged" false="" merged} \
+ ~{true="--everything" false="" everything} \
+ ~{true="--symbol" false="" symbol}
+
+ VEP_EXIT_CODE=$?
+ set -e
+ # Cleanup the tar extract to save filesystem space
+ rm -rf vep_cache
+
+ exit $VEP_EXIT_CODE
+ >>>
+
+ output {
+ File outputFile = outputPath
+ File statsHtml = outputPath + "_summary.html"
+ File statsTxt = outputPath + "_summary.txt"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # input
+ inputFile: {description: "The VCF to annotate.", category: "required"}
+ outputPath: {description: "Where to put the output file", category: "advanced"}
+ cacheTar: {description: "A TAR archive containing the cache. The TAR archives from the VEP website work (http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html)", category: "required"}
+ pluginsTar: {description: "A TAR file with custom plugins.", category: "advanced"}
+ species: {description: "Which species cache to use", category: "common"}
+ plugins: {description: "Which plugins to use", category: "common"}
+ refseq: {description: "Use the refseq cache", category: "common"}
+ merged: {description: "Use the merged cache", category: "common"}
+ everything: {description: "Use all annotation sources bundeld with vep.", category: "common"}
+ symbol: {description: "Add the gene symbol to the output where available", category: "advanced"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # output
+ outputFile: {description: "The annotated VEP VCF file."}
+ statsHtml: {description: "The VEP summary stats HTML file."}
+ statsTxt: {description: "The VEP summary stats TXT file."}
+ }
+}
diff --git a/vt.wdl b/vt.wdl
index d4c134b9..635641e9 100644
--- a/vt.wdl
+++ b/vt.wdl
@@ -1,6 +1,6 @@
version 1.0
-# Copyright (c) 2020 Sequencing Analysis Support Core - Leiden University Medical Center
+# Copyright (c) 2020 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -26,23 +26,40 @@ task Normalize {
File inputVCFIndex
File referenceFasta
File referenceFastaFai
- String outputPath = "./vt/normalized_decomposed.vcf"
- String dockerImage = "quay.io/biocontainers/vt:0.57721--hdf88d34_2"
- String memory = "4G"
- Int timeMinutes = 30
+ Boolean ignoreMaskedRef = false
+ String outputPath = "./vt/normalized_decomposed.vcf.gz"
+ String? filterExpression
+
+ Int compressionLevel = 1
+
+ String memory = "4GiB"
+ Int timeMinutes = 10 + ceil(size(inputVCF, "GiB") * 240)
+ String dockerImage = "quay.io/biocontainers/vt:0.57721--h2419454_12"
}
command {
- set -e
+ set -eo pipefail
mkdir -p "$(dirname ~{outputPath})"
- vt normalize ~{inputVCF} -r ~{referenceFasta} | vt decompose -s - -o ~{outputPath}
+ vt view -h \
+ ~{"-f '" + filterExpression}~{true="'" false="" defined(filterExpression)} \
+ ~{inputVCF} \
+ | vt normalize - \
+ -r ~{referenceFasta} \
+ ~{true="-m " false="" ignoreMaskedRef} \
+ | vt decompose -s - \
+ | vt view - \
+ -c ~{compressionLevel} \
+ -o ~{outputPath}
+ vt index ~{outputPath}
}
output {
File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
}
runtime {
+ cpu: 1
memory: memory
time_minutes: timeMinutes
docker: dockerImage
@@ -52,12 +69,19 @@ task Normalize {
# inputs
inputVCF: {description: "The VCF file to process.", category: "required"}
inputVCFIndex: {description: "The index of the VCF file to be processed.", category: "required"}
- outputPath: {description: "The location the output VCF file should be written.", category: "common"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- memory: {description: "The memory required to run the programs", category: "advanced"}
+ ignoreMaskedRef: {description: "Warns but does not exit when REF is inconsistent with masked reference sequence for non SNPs.", category: "advanced"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ filterExpression: {description: "See https://genome.sph.umich.edu/wiki/Vt#Filters for valid expressions.", category: "common"}
+ compressionLevel: {description: "Compression level for the out vcf.gz file.", category: "advanced"}
+
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "Normalized and decomposed VCF file."}
+ outputVcfIndex: {description: "Index for normalized and decomposed VCF file."}
}
}
-
diff --git a/whatshap.wdl b/whatshap.wdl
new file mode 100644
index 00000000..b491f566
--- /dev/null
+++ b/whatshap.wdl
@@ -0,0 +1,233 @@
+version 1.0
+
+# Copyright (c) 2018 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Phase {
+ input {
+ String outputVCF
+ File vcf
+ File vcfIndex
+ File phaseInput
+ File phaseInputIndex
+
+ File? reference
+ File? referenceIndex
+ String? tag
+ String? algorithm
+ Boolean? indels
+ String? sample
+ String? chromosome
+ String? threshold
+ String? ped
+
+ String memory = 2 + ceil(size(phaseInput, "G") / 20 )
+ Int timeMinutes = 400 + ceil(size(phaseInput, "G") * 0.9 )
+
+ # Whatshap 1.0, tabix 0.2.5.
+ String dockerImage = "quay.io/biocontainers/mulled-v2-5c61fe1d8c284dd05d26238ce877aa323205bf82:89b4005d04552bdd268e8af323df83357e968d83-0"
+ }
+
+ command {
+ set -e
+
+ mkdir -p $(dirname ~{outputVCF})
+
+ whatshap phase \
+ ~{vcf} \
+ ~{phaseInput} \
+ ~{if defined(outputVCF) then ("--output " + '"' + outputVCF + '"') else ""} \
+ ~{if defined(reference) then ("--reference " + '"' + reference + '"') else ""} \
+ ~{if defined(tag) then ("--tag " + '"' + tag + '"') else ""} \
+ ~{if defined(algorithm) then ("--algorithm " + '"' + algorithm + '"') else ""} \
+ ~{true="--indels" false="" indels} \
+ ~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""} \
+ ~{if defined(chromosome) then ("--chromosome " + '"' + chromosome + '"') else ""} \
+ ~{if defined(threshold) then ("--threshold " + '"' + threshold + '"') else ""} \
+ ~{if defined(ped) then ("--ped " + '"' + ped + '"') else ""}
+
+ tabix -p vcf ~{outputVCF}
+ }
+
+ output {
+ File phasedVCF = outputVCF
+ File phasedVCFIndex = outputVCF + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ outputVCF: {description: "Output VCF file. Add .gz to the file name to get compressed output. If omitted, use standard output.", category: "common"}
+ vcf: {description: "VCF or BCF file with variants to be phased (can be gzip-compressed).", category: "required"}
+ vcfIndex: {description: "Index for the VCF or BCF file with variants to be phased.", category: "required"}
+ phaseInput: {description: "BAM, CRAM, VCF or BCF file(s) with phase information, either through sequencing reads (BAM, CRAM) or through phased blocks (VCF, BCF).", category: "required"}
+ phaseInputIndex: {description: "Index of BAM, CRAM, VCF or BCF file(s) with phase information.", category: "required"}
+ reference: {description: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created.", category: "common"}
+ referenceIndex: {description: "Index of reference file.", category: "common"}
+ tag: {description: "Store phasing information with PS tag (standardized) or HP tag (used by GATK ReadBackedPhasing) (default: {description: PS).", category: "common"}
+ algorithm: {description: "Phasing algorithm to use (default: {description: whatshap).", category: "advanced"}
+ indels: {description: "Also phase indels (default: {description: do not phase indels).", category: "common"}
+ sample: {description: "Name of a sample to phase. If not given, all samples in the input VCF are phased. Can be used multiple times.", category: "common"}
+ chromosome: {description: "Name of chromosome to phase. If not given, all chromosomes in the input VCF are phased. Can be used multiple times.", category: "common"}
+ threshold: {description: "The threshold of the ratio between the probabilities that a pair of reads come from the same haplotype and different haplotypes in the read merging model (default: {description: 1000000).", category: "advanced"}
+ ped: {description: "Use pedigree information in PED file to improve phasing (switches to PedMEC algorithm). Columns 2, 3, 4 must refer to child, mother, and father sample names as used in the VCF and BAM/CRAM. Other columns are ignored.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ phasedVCF: {description: "VCF file containing phased variants."}
+ phasedVCFIndex: {description: "Index of phased VCF file."}
+ }
+}
+
+task Stats {
+ input {
+ File vcf
+
+ String? gtf
+ String? sample
+ String? tsv
+ String? blockList
+ String? chromosome
+
+ String memory = "4GiB"
+ Int timeMinutes = 30
+ # Whatshap 1.0, tabix 0.2.5.
+ String dockerImage = "quay.io/biocontainers/mulled-v2-5c61fe1d8c284dd05d26238ce877aa323205bf82:89b4005d04552bdd268e8af323df83357e968d83-0"
+ }
+
+ command {
+ set -e
+
+ mkdir -p $(dirname ~{tsv})
+
+ whatshap stats \
+ ~{vcf} \
+ ~{if defined(gtf) then ("--gtf " + '"' + gtf + '"') else ""} \
+ ~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""} \
+ ~{if defined(tsv) then ("--tsv " + '"' + tsv + '"') else ""} \
+ ~{if defined(blockList) then ("--block-list " + '"' + blockList + '"') else ""} \
+ ~{if defined(chromosome) then ("--chromosome " + '"' + chromosome + '"') else ""}
+ }
+
+ output {
+ File? phasedGTF = gtf
+ File? phasedTSV = tsv
+ File? phasedBlockList = blockList
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ vcf: {description: "Phased VCF file.", category: "required"}
+ gtf: {description: "Write phased blocks to GTF file.", category: "common"}
+ sample: {description: "Name of the sample to process. If not given, use first sample found in VCF.", category: "common"}
+ tsv: {description: "Filename to write statistics to (tab-separated).", category: "common"}
+ blockList: {description: "Filename to write list of all blocks to (one block per line).", category: "advanced"}
+ chromosome: {description: "Name of chromosome to process. If not given, all chromosomes in the input VCF are considered.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ phasedGTF: {description: "Phasing statistics for a single VCF file."}
+ phasedTSV: {description: "Statistics in a tab-separated value format."}
+ phasedBlockList: {description: "List of the total number of phase sets/blocks."}
+ }
+}
+
+task Haplotag {
+ input {
+ File vcf
+ File vcfIndex
+ File alignments
+ File alignmentsIndex
+ String outputFile
+
+ File? reference
+ File? referenceFastaIndex
+ String? regions
+ String? sample
+
+ String memory = 2 + ceil(size(alignments, "G") / 50 )
+ Int timeMinutes = 50 + ceil(size(alignments, "G") * 2 )
+
+ # Whatshap 1.0, tabix 0.2.5.
+ String dockerImage = "quay.io/biocontainers/mulled-v2-5c61fe1d8c284dd05d26238ce877aa323205bf82:89b4005d04552bdd268e8af323df83357e968d83-0"
+ }
+
+ command {
+ set -e
+
+ mkdir -p $(dirname ~{outputFile})
+
+ whatshap haplotag \
+ ~{vcf} \
+ ~{alignments} \
+ ~{if defined(outputFile) then ("--output " + '"' + outputFile+ '"') else ""} \
+ ~{if defined(reference) then ("--reference " + '"' + reference + '"') else ""} \
+ ~{if defined(regions) then ("--regions " + '"' + regions + '"') else ""} \
+ ~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""}
+
+ python3 -c "import pysam; pysam.index('~{outputFile}')"
+ }
+
+ output {
+ File bam = outputFile
+ File bamIndex = outputFile + ".bai"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ vcf: {description: "VCF file with phased variants (must be gzip-compressed and indexed).", category: "required"}
+ vcfIndex: {description: "Index for the VCF or BCF file with variants to be phased.", category: "required"}
+ alignments: {description: "File (BAM/CRAM) with read alignments to be tagged by haplotype.", category: "required"}
+ alignmentsIndex: {description: "Index for the alignment file.", category: "required"}
+ outputFile: {description: "Output file. If omitted, use standard output.", category: "required"}
+ reference: {description: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created.", category: "common"}
+ referenceFastaIndex: {description: "Index for the reference file.", category: "common"}
+ regions: {description: "Specify region(s) of interest to limit the tagging to reads/variants overlapping those regions. You can specify a space-separated list of regions in the form of chrom:start-end, chrom (consider entire chromosome), or chrom:start (consider region from this start to end of chromosome).", category: "advanced"}
+ sample: {description: "Name of a sample to phase. If not given, all samples in the input VCF are phased. Can be used multiple times.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ bam: {description: "BAM file containing tagged reads for haplotype."}
+ bamIndex: {description: "Index of the tagged BAM file."}
+ }
+}
diff --git a/wisestork.wdl b/wisestork.wdl
index 0fd812b1..bef54e27 100644
--- a/wisestork.wdl
+++ b/wisestork.wdl
@@ -22,13 +22,16 @@ version 1.0
task Count {
input {
- Int? binSize
- File reference
- File referenceIndex
- File? binFile
File inputBam
File inputBamIndex
+ File reference
+ File referenceIndex
String outputBed = "output.bed"
+
+ Int? binSize
+ File? binFile
+
+ String memory = "2GiB"
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
@@ -48,21 +51,25 @@ task Count {
}
runtime {
+ memory: memory
docker: dockerImage
}
}
task GcCorrect {
input {
- Int? binSize
File reference
File referenceIndex
- File? binFile
File inputBed
String outputBed = "output.bed"
+
+ Int? binSize
+ File? binFile
Float? fracN
Int? iter
Float? fracLowess
+
+ String memory = "2GiB"
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
@@ -85,19 +92,23 @@ task GcCorrect {
}
runtime {
+ memory: memory
docker: dockerImage
}
}
task Newref {
input {
- Int? binSize
File reference
File referenceIndex
- File? binFile
Array[File]+ inputBeds
String outputBed = "output.bed"
+
+ Int? binSize
+ File? binFile
Int? nBins
+
+ Int memory = 2 + ceil(length(inputBeds) * 0.15)
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
@@ -106,36 +117,37 @@ task Newref {
mkdir -p $(dirname ~{outputBed})
wisestork newref \
~{"--binsize " + binSize} \
- --reference ~{reference} \
- ~{"--bin-file " + binFile} \
- --output ~{outputBed} \
- -I ~{sep=" -I " inputBeds} \
- ~{"--n-bins " + nBins}
+ --reference ~{reference} \
+ ~{"--bin-file " + binFile} \
+ --output ~{outputBed} \
+ -I ~{sep=" -I " inputBeds} \
+ ~{"--n-bins " + nBins}
}
output {
File bedFile = outputBed
}
- Int memory = 2 + ceil(length(inputBeds) * 0.15)
-
runtime {
+ memory: "~{memory}GiB"
docker: dockerImage
- memory: "~{memory}G"
}
}
task Zscore {
input {
- Int? binSize
File reference
File referenceIndex
- File? binFile
File inputBed
File inputBedIndex
File dictionaryFile
File dictionaryFileIndex
String outputBed = "output.bed"
+
+ Int? binSize
+ File? binFile
+
+ String memory = "2GiB"
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
@@ -156,7 +168,7 @@ task Zscore {
}
runtime {
+ memory: memory
docker: dockerImage
}
}
-