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Merge branch 'master' into antismash_db_output
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commit
f03afbd337
2 changed files with 13 additions and 5 deletions
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@ -11,12 +11,13 @@ process TRIMGALORE {
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.fq.gz") , emit: reads
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tuple val(meta), path("*report.txt"), emit: log
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path "versions.yml" , emit: versions
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tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
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tuple val(meta), path("*report.txt") , emit: log
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.html"), emit: html optional true
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tuple val(meta), path("*.zip") , emit: zip optional true
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tuple val(meta), path("*unpaired*.fq.gz") , emit: unpaired, optional: true
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tuple val(meta), path("*.html") , emit: html , optional: true
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tuple val(meta), path("*.zip") , emit: zip , optional: true
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when:
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task.ext.when == null || task.ext.when
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@ -52,6 +53,7 @@ process TRIMGALORE {
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$c_r1 \\
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$tpc_r1 \\
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${prefix}.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
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@ -73,6 +75,7 @@ process TRIMGALORE {
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$tpc_r2 \\
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${prefix}_1.fastq.gz \\
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${prefix}_2.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
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@ -37,6 +37,11 @@ output:
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List of input adapter trimmed FastQ files of size 1 and 2 for
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single-end and paired-end data, respectively.
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pattern: "*.{fq.gz}"
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- unpaired:
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type: file
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description: |
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FastQ files containing unpaired reads from read 1 or read 2
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pattern: "*unpaired*.fq.gz"
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- html:
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type: file
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description: FastQC report (optional)
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