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Merge branch 'master' into antismash_db_output

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James A. Fellows Yates 2022-04-27 08:30:50 +02:00 committed by GitHub
commit f03afbd337
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2 changed files with 13 additions and 5 deletions
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13
modules/trimgalore/main.nf
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@ -11,12 +11,13 @@ process TRIMGALORE {
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.fq.gz") , emit: reads
tuple val(meta), path("*report.txt"), emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
tuple val(meta), path("*report.txt") , emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*.html"), emit: html optional true
tuple val(meta), path("*.zip") , emit: zip optional true
tuple val(meta), path("*unpaired*.fq.gz") , emit: unpaired, optional: true
tuple val(meta), path("*.html") , emit: html , optional: true
tuple val(meta), path("*.zip") , emit: zip , optional: true
when:
task.ext.when == null || task.ext.when
@ -52,6 +53,7 @@ process TRIMGALORE {
$c_r1 \\
$tpc_r1 \\
${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
@ -73,6 +75,7 @@ process TRIMGALORE {
$tpc_r2 \\
${prefix}_1.fastq.gz \\
${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')

5
modules/trimgalore/meta.yml
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@ -37,6 +37,11 @@ output:
List of input adapter trimmed FastQ files of size 1 and 2 for
single-end and paired-end data, respectively.
pattern: "*.{fq.gz}"
- unpaired:
type: file
description: |
FastQ files containing unpaired reads from read 1 or read 2
pattern: "*unpaired*.fq.gz"
- html:
type: file
description: FastQC report (optional)