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8c00897853
* Add AdapterRemovalFixPrefix * Prettifying Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
def VERSION = '0.05'
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process ADAPTERREMOVALFIXPREFIX {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
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'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
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input:
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tuple val(meta), path(fastq)
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output:
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tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
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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 ?: "${meta.id}"
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if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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"""
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AdapterRemovalFixPrefix \\
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$fastq \\
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$args \\
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| gzip > ${prefix}.fq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremovalfixprefix: $VERSION
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END_VERSIONS
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"""
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}
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