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* add bamsormadup * fix yaml * add test.yml * Update tests/modules/biobambam/bamsormadup/test.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * test meta.yaml: remove md5sums * Tool bamsormadup: - add (optional) reference input - add bam index ouput - add cram output option - make metrics output: more general * fix input and output formats * update input file description * drop sam output, goes against nf-core regs; add input check for cram files * fix typo * Update modules/biobambam/bamsormadup/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * improve ref fasta name * fix if else shorthand * fix syntax error * kind of fix tests * set fixed suffix for metrics file to keep it in line with picard and bammarkduplicates2 * fix command line * update test.yml * add support for multiple input bams * Update modules/biobambam/bamsormadup/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/biobambam/bamsormadup/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/biobambam/bamsormadup/test.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
process BIOBAMBAM_BAMSORMADUP {
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tag "$meta.id"
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label "process_medium"
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conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
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input:
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tuple val(meta), path(bams)
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path(fasta)
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output:
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tuple val(meta), path("*.{bam,cram}") ,emit: bam
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tuple val(meta), path("*.bam.bai") ,optional:true, emit: bam_index
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tuple val(meta), path("*.metrics.txt") ,emit: metrics
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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 ?: "${meta.id}"
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def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
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def input_string = bams.join(" I=")
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if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."
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"""
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bamcat \\
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I=${input_string} \\
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level=0 \\
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| bamsormadup \\
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$args \\
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M=${prefix}.metrics.txt \\
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tmpfile=$prefix \\
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threads=$task.cpus \\
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> ${prefix}.${suffix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bamcat: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
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bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
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END_VERSIONS
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"""
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}
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