61 lines
2 KiB
Text
Generated
61 lines
2 KiB
Text
Generated
process FASTQC {
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tag "$meta.id"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
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'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.html"), emit: html
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tuple val(meta), path("*.zip") , emit: zip
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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// Make list of old name and new name pairs to use for renaming in the bash while loop
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def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
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def rename_to = old_new_pairs*.join(' ').join(' ')
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def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
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def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
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// FastQC memory value allowed range (100 - 10000)
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def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
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"""
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printf "%s %s\\n" $rename_to | while read old_name new_name; do
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[ -f "\${new_name}" ] || ln -s \$old_name \$new_name
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done
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fastqc \\
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$args \\
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--threads $task.cpus \\
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--memory $fastqc_memory \\
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$renamed_files
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.html
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touch ${prefix}.zip
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
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END_VERSIONS
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"""
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}
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