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42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
process SAMTOOLS_CONVERT {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ 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), path(index)
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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("*.{cram,bam}"), path("*.{crai,bai}") , emit: aligned_index
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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 output_extension = input.getExtension() == "bam" ? "cram" : "bam"
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"""
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samtools view \\
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--threads ${task.cpus} \\
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--reference ${fasta} \\
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$args \\
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$input \\
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-o ${prefix}.${output_extension}
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samtools index -@${task.cpus} ${prefix}.${output_extension}
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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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