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48 lines
1.6 KiB
Plaintext
48 lines
1.6 KiB
Plaintext
process FASTQC {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
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'quay.io/biocontainers/fastqc:0.11.9--0' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.html"), emit: html
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tuple val(meta), path("*.zip") , emit: zip
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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// Add soft-links to original FastQs for consistent naming in pipeline
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (meta.single_end) {
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"""
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[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
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fastqc $args --threads $task.cpus ${prefix}.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
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END_VERSIONS
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"""
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} else {
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"""
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[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
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END_VERSIONS
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"""
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}
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}
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