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35 lines
1,022 B
Text
35 lines
1,022 B
Text
process PYDAMAGE_ANALYZE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' :
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'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(bam), path(bai)
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output:
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tuple val(meta), path("pydamage_results/pydamage_results.csv"), emit: csv
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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 ?: "${meta.id}"
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"""
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pydamage \\
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analyze \\
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$args \\
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-p $task.cpus \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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pydamage: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
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END_VERSIONS
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"""
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}
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