2021-03-23 13:37:53 +00:00
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process ALLELECOUNTER {
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tag "$meta.id"
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label 'process_low'
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2021-07-28 08:10:44 +00:00
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conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
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2021-11-26 07:58:40 +00:00
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
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'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"
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2021-03-23 13:37:53 +00:00
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input:
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2021-11-02 16:00:25 +00:00
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tuple val(meta), path(input), path(input_index)
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2021-03-23 13:37:53 +00:00
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path loci
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2021-11-02 16:00:25 +00:00
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path fasta
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2021-03-23 13:37:53 +00:00
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output:
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tuple val(meta), path("*.alleleCount"), emit: allelecount
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2021-10-01 13:04:56 +00:00
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path "versions.yml" , emit: versions
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2021-03-23 13:37:53 +00:00
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script:
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2021-11-26 07:58:40 +00:00
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def args = task.ext.args ?: ''
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def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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2021-11-02 16:00:25 +00:00
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def reference_options = fasta ? "-r $fasta": ""
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2021-03-23 13:37:53 +00:00
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"""
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alleleCounter \\
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2021-11-26 07:58:40 +00:00
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$args \\
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2021-03-23 13:37:53 +00:00
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-l $loci \\
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2021-11-02 16:00:25 +00:00
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-b $input \\
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$reference_options \\
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2021-03-23 13:37:53 +00:00
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-o ${prefix}.alleleCount
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2021-09-27 08:41:24 +00:00
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cat <<-END_VERSIONS > versions.yml
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2021-11-26 07:58:40 +00:00
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"${task.process}":
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allelecounter: \$(alleleCounter --version)
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2021-09-27 08:41:24 +00:00
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END_VERSIONS
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2021-03-23 13:37:53 +00:00
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"""
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}
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