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https://github.com/MillironX/nf-core_modules.git
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fd5f6f5f4f
* revert changes to modules * fix tests * fix kraken2 * fix untar * fix cat * add blank lines * fix typo
51 lines
1.4 KiB
Text
51 lines
1.4 KiB
Text
process TIDDIT_COV {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
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'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
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input:
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tuple val(meta), path(bam)
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path fasta
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output:
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tuple val(meta), path("*.tab"), optional: true, emit: cov
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tuple val(meta), path("*.wig"), optional: true, emit: wig
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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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def reference = fasta ? "--ref $fasta" : ""
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"""
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tiddit \\
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--cov \\
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-o $prefix \\
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$args \\
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--bam $bam \\
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$reference
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.wig
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touch ${prefix}.tab
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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