这是indexloc提供的服务，不要输入任何密码
Skip to content

Update VT to also create index #339

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Apr 29, 2025
Merged

Update VT to also create index #339

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
847ad71
Update vt to allow a filter expression and compressed indexed output
rhpvorderman Apr 9, 2025
57018dd
Properly quote vt filter
rhpvorderman Apr 11, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ that users understand how the changes affect the new version.

version 6.0.0-dev
---------------------------
+ Update vt task to allow a filter expression and compress and index the output.
+ MultiQC image updated to version 1.28
+ Samtools merge now has options added for merging RG and PG headers.
+ Samtools merge default thread count increased based on the number of files.
Expand Down
28 changes: 22 additions & 6 deletions vt.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,27 +27,39 @@ task Normalize {
File referenceFasta
File referenceFastaFai
Boolean ignoreMaskedRef = false
String outputPath = "./vt/normalized_decomposed.vcf"
String outputPath = "./vt/normalized_decomposed.vcf.gz"
String? filterExpression

Int compressionLevel = 1

String memory = "4GiB"
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/vt:0.57721--hdf88d34_2"
Int timeMinutes = 10 + ceil(size(inputVCF, "GiB") * 240)
String dockerImage = "quay.io/biocontainers/vt:0.57721--h2419454_12"
}

command {
set -eo pipefail
mkdir -p "$(dirname ~{outputPath})"
vt normalize ~{inputVCF} \
vt view -h \
~{"-f '" + filterExpression}~{true="'" false="" defined(filterExpression)} \
~{inputVCF} \
| vt normalize - \
-r ~{referenceFasta} \
~{true="-m " false="" ignoreMaskedRef} \
| vt decompose -s - -o ~{outputPath}
| 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
Expand All @@ -61,11 +73,15 @@ task Normalize {
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
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 & decomposed VCF file."}
outputVcf: {description: "Normalized and decomposed VCF file."}
outputVcfIndex: {description: "Index for normalized and decomposed VCF file."}
}
}
Loading