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02892ef654
* add base code from samblaster * added test yml * fixing versions files, should this be the cause of online lint failures * removed tmp files that shouldn't be there * fixing output file name - 1 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 2 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 3 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 4 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 5 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 6 * fixed indent * fixed input name and updated test.yml file with new name Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
1.8 KiB
Text
42 lines
1.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process SAMBLASTER {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0"
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}
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use the suffix option to disambiguate"
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"""
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samtools view -h $options.args2 $bam | \\
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samblaster $options.args | \\
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samtools view $options.args3 -Sb - >${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( samblaster -h 2>&1 | head -n 1 | sed 's/^samblaster: Version //' )
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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