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Bedtools wa/wb/s #333

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Merged
merged 1 commit into from
Mar 28, 2025
Merged

Bedtools wa/wb/s #333

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -22,6 +22,7 @@ version 6.0.0-dev
+ Use softlinks to localise the database for centrifuge.
+ Added the FastqFilter task.
+ Added a new input `revcomp` to cutadapt to set the `--revcomp` flag, defaults to `false`.
+ Update `bedtools.Intersect` to support `-wa`, `-wb`, and `-s` flags.

version 5.2.0
---------------------------
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13 changes: 13 additions & 0 deletions bedtools.wdl
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Expand Up @@ -267,6 +267,10 @@ task Intersect {

File? faidx # Giving a faidx file will set the sorted option.

Boolean writeA = false
Boolean writeB = false
Boolean stranded = false

String memory = "~{512 + ceil(size([regionsA, regionsB], "MiB"))}MiB"
Int timeMinutes = 1 + ceil(size([regionsA, regionsB], "GiB"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
Expand All @@ -276,10 +280,14 @@ task Intersect {

command {
set -e
mkdir -p "$(dirname ~{outputBed})"
~{"cut -f1,2 " + faidx} ~{true="> sorted.genome" false ="" sorted}
bedtools intersect \
-a ~{regionsA} \
-b ~{regionsB} \
~{true="-wa" false="" writeA} \
~{true="-wb" false="" writeB} \
~{true="-s" false="" stranded} \
~{true="-sorted" false="" sorted} \
~{true="-g sorted.genome" false="" sorted} \
> ~{outputBed}
Expand All @@ -301,6 +309,11 @@ task Intersect {
regionsB: {description: "Region file b to intersect.", category: "required"}
outputBed: {description: "The path to write the output to.", category: "advanced"}
faidx: {description: "The fasta index (.fai) file that is used to create the genome file required for sorted output. Implies sorted option.", category: "common"}

writeA: {description: "Write the original entry in A for each overlap.", category: "advanced"}
writeB: {description: "Write the original entry in B for each overlap. Useful for knowing what A overlaps.", category: "advanced"}
stranded: {description: "Force “strandedness”. That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.", category: "advanced"}

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"}
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