From f9b14508e1baf862943d48c293137d7934e5054e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 7 Jul 2025 11:27:17 +0200 Subject: [PATCH 1/3] bump bedtools sort --- bedtools.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bedtools.wdl b/bedtools.wdl index a5d8aab3..50acd42d 100644 --- a/bedtools.wdl +++ b/bedtools.wdl @@ -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 { From c8fbb60c214cb3defe74b71aa60df6eefbae594a Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 7 Jul 2025 11:28:18 +0200 Subject: [PATCH 2/3] document --- CHANGELOG.md | 1 + bedtools.wdl | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e0b036ac..920993ec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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`. + 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. diff --git a/bedtools.wdl b/bedtools.wdl index 50acd42d..7fcce28f 100644 --- a/bedtools.wdl +++ b/bedtools.wdl @@ -224,7 +224,7 @@ task Sort { ~{true="-chrThenScoreA" false="" chrThenScoreA} \ ~{true="-chrThenScoreD" false="" chrThenScoreD} \ ~{"-g " + genome} \ - ~{"-faidx" + faidx} \ + ~{"-faidx " + faidx} \ > ~{outputBed} } From 633d0bc76ffb27f09b957e7eb26153a8f3d5edac Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 7 Jul 2025 12:33:54 +0200 Subject: [PATCH 3/3] Add no name check support, requiring bumping Intersect as well --- bedtools.wdl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/bedtools.wdl b/bedtools.wdl index 7fcce28f..64fccc7b 100644 --- a/bedtools.wdl +++ b/bedtools.wdl @@ -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) @@ -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} } @@ -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"}