2021-01-29 16:18:45 +00:00
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process SAMTOOLS_VIEW {
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tag "$meta.id"
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2021-03-16 17:16:47 +00:00
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label 'process_medium'
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2021-01-29 16:18:45 +00:00
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2022-04-11 12:26:28 +00:00
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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2021-11-26 07:58:40 +00:00
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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2022-04-11 12:26:28 +00:00
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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2021-01-29 16:18:45 +00:00
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input:
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2021-10-29 11:01:05 +00:00
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tuple val(meta), path(input)
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path fasta
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2021-01-29 16:18:45 +00:00
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output:
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2021-11-18 21:24:47 +00:00
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tuple val(meta), path("*.bam") , emit: bam , optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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path "versions.yml" , emit: versions
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2021-01-29 16:18:45 +00:00
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2022-02-04 08:53:32 +00:00
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when:
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task.ext.when == null || task.ext.when
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2021-01-29 16:18:45 +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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2022-01-11 21:39:21 +00:00
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def args2 = task.ext.args2 ?: ''
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2021-12-02 12:39:55 +00:00
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def prefix = task.ext.prefix ?: "${meta.id}"
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2021-10-29 11:01:05 +00:00
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def reference = fasta ? "--reference ${fasta} -C" : ""
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def file_type = input.getExtension()
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2022-01-07 17:52:39 +00:00
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if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
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2021-01-29 16:18:45 +00:00
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"""
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2022-01-07 17:52:39 +00:00
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samtools \\
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view \\
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--threads ${task.cpus-1} \\
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${reference} \\
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$args \\
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$input \\
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2022-01-11 21:39:21 +00:00
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$args2 \\
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2022-01-07 17:52:39 +00:00
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> ${prefix}.${file_type}
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2021-11-18 21:24:47 +00:00
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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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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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2021-09-27 08:41:24 +00:00
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END_VERSIONS
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2021-01-29 16:18:45 +00:00
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"""
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2021-01-29 17:01:58 +00:00
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}
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