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251015c8ba
* Add samtools index to yara_mapper module. * samtools sort required for index Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
65 lines
2.4 KiB
Text
65 lines
2.4 KiB
Text
process YARA_MAPPER {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.12" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' :
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'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' }"
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input:
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tuple val(meta), path(reads)
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path index
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output:
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tuple val(meta), path("*.mapped.bam"), emit: bam
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tuple val(meta), path("*.mapped.bam.bai"), emit: bai
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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 ?: "${meta.id}"
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if (meta.single_end) {
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"""
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yara_mapper \\
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$args \\
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-t $task.cpus \\
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-f bam \\
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${index}/yara \\
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$reads | samtools view -@ $task.cpus -hb -F4 | samtools sort -@ $task.cpus > ${prefix}.mapped.bam
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samtools index -@ $task.cpus ${prefix}.mapped.bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
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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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} else {
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"""
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yara_mapper \\
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$args \\
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-t $task.cpus \\
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-f bam \\
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${index}/yara \\
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${reads[0]} \\
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${reads[1]} > output.bam
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samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_1.mapped.bam
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samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_2.mapped.bam
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samtools index -@ $task.cpus ${prefix}_1.mapped.bam
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samtools index -@ $task.cpus ${prefix}_2.mapped.bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
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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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}
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