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bump bedtools sort #346

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Merged
merged 5 commits into from
Jul 29, 2025
Merged

bump bedtools sort #346

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f9b1450
bump bedtools sort
hexylena Jul 7, 2025
c8fbb60
document
hexylena Jul 7, 2025
633d0bc
Add no name check support, requiring bumping Intersect as well
hexylena Jul 7, 2025
ed38777
Merge branch 'develop' into churra-scylla
hexylena Jul 22, 2025
5a97180
Merge branch 'develop' into churra-scylla
hexylena Jul 29, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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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
---------------------------
+ bedtools.Sort: bumped container version to permit use of `faidx`.
+ Add a task for bcftools norm.
+ Add support for outputting compressed files to snpeff and snpsift.
+ Fixed an issue with the parameter_meta section of bcftools annotate
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9 changes: 6 additions & 3 deletions bedtools.wdl
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Expand Up @@ -209,7 +209,7 @@ task Sort {

String memory = "~{512 + ceil(size(inputBed, "MiB"))}MiB"
Int timeMinutes = 1 + ceil(size(inputBed, "GiB"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
String dockerImage = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2"
}

command {
Expand All @@ -224,7 +224,7 @@ task Sort {
~{true="-chrThenScoreA" false="" chrThenScoreA} \
~{true="-chrThenScoreD" false="" chrThenScoreD} \
~{"-g " + genome} \
~{"-faidx" + faidx} \
~{"-faidx " + faidx} \
> ~{outputBed}
}

Expand Down Expand Up @@ -270,10 +270,11 @@ task Intersect {
Boolean writeA = false
Boolean writeB = false
Boolean stranded = false
Boolean nonamecheck = 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"
String dockerImage = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2"
}

Boolean sorted = defined(faidx)
Expand All @@ -289,6 +290,7 @@ task Intersect {
~{true="-wb" false="" writeB} \
~{true="-s" false="" stranded} \
~{true="-sorted" false="" sorted} \
~{true="-nonamecheck" false="" nonamecheck} \
~{true="-g sorted.genome" false="" sorted} \
> ~{outputBed}
}
Expand All @@ -313,6 +315,7 @@ task Intersect {
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"}
nonamecheck: {description: "Disable the bedtools intersect name check. This is used to catch chr1 vs chr01 or chr1 vs 1 naming inconsistencies. However, it throws an error for GIAB hg38 which has capital letters. https://github.com/arq5x/bedtools2/issues/648", 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"}
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