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38 lines
1.1 KiB
Plaintext
38 lines
1.1 KiB
Plaintext
process SAMTOOLS_FASTA {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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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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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*.fasta.gz"), emit: fasta
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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 endedness = meta.single_end ? "-0 ${prefix}.fasta.gz" : "-1 ${prefix}_1.fasta.gz -2 ${prefix}_2.fasta.gz"
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"""
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samtools \\
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fasta \\
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$args \\
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--threads ${task.cpus-1} \\
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$endedness \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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}
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