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https://github.com/MillironX/nf-core_modules.git
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682f789f93
* Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
67 lines
2.4 KiB
Text
67 lines
2.4 KiB
Text
process PICARD_COLLECTMULTIPLEMETRICS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.27.4--hdfd78af_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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path fai
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output:
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tuple val(meta), path("*_metrics"), emit: metrics
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tuple val(meta), path("*.pdf") , emit: pdf
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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 ? "--REFERENCE_SEQUENCE ${fasta}" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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picard \\
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-Xmx${avail_mem}g \\
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CollectMultipleMetrics \\
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$args \\
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--INPUT $bam \\
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--OUTPUT ${prefix}.CollectMultipleMetrics \\
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$reference
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics
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touch ${prefix}.CollectMultipleMetrics.insert_size_metrics
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touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf
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touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics
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touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf
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touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf
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touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf
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touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf
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touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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}
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