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Collate fastq file before splitting #331

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Merged
merged 2 commits into from
Mar 28, 2025
Merged

Collate fastq file before splitting #331

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38c5c9a
Collate fastq file before splitting
hexylena Mar 25, 2025
c8ecc6c
Merge branch 'develop' into fastq-collation
rhpvorderman Mar 28, 2025
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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`.
+ Fixed bug whereby `samtools.Fastq` could produce out of sync R1/R2 when used with an unsorted bam input. `samtools collate` is now used by default to group reads by readname in order to avoid this issue.
+ New samtools task: split.
+ Update `bedtools.Intersect` to support `-wa`, `-wb`, and `-s` flags.

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4 changes: 2 additions & 2 deletions samtools.wdl
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Expand Up @@ -174,6 +174,7 @@ task Fastq {
command {
set -e
mkdir -p "$(dirname ~{outputRead1})"
samtools collate -u -O ~{inputBam} | \
samtools fastq \
~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
~{"-2 " + outputRead2} \
Expand All @@ -184,8 +185,7 @@ task Fastq {
~{true="-N" false="-n" appendReadNumber} \
~{true="-O" false="" outputQuality} \
~{"-c " + compressionLevel} \
~{"--threads " + threads} \
~{inputBam}
~{"--threads " + threads}
}

output {
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