2021-02-12 12:00:02 +00:00
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process BWAMEM2_MEM {
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tag "$meta.id"
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label 'process_high'
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2021-03-25 09:24:21 +00:00
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conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null)
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2021-11-26 07:58:40 +00:00
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' :
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'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' }"
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2021-02-12 12:00:02 +00:00
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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("*.bam"), emit: bam
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2021-10-01 13:04:56 +00:00
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path "versions.yml" , emit: versions
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2021-02-12 12:00:02 +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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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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2021-02-12 12:00:02 +00:00
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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2021-09-27 21:10:37 +00:00
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bwa-mem2 \\
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mem \\
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2021-11-26 07:58:40 +00:00
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$args \\
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2021-02-12 12:00:02 +00:00
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$read_group \\
|
2021-09-30 08:26:52 +00:00
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-t $task.cpus \\
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2021-02-12 12:00:02 +00:00
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\$INDEX \\
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$reads \\
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2021-11-26 07:58:40 +00:00
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| samtools view $args2 -@ $task.cpus -bhS -o ${prefix}.bam -
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2021-02-12 12:00:02 +00:00
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2021-09-27 08:41:24 +00:00
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cat <<-END_VERSIONS > versions.yml
|
2021-11-26 07:58:40 +00:00
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"${task.process}":
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bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
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2021-09-28 13:37:47 +00:00
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
2021-09-27 08:41:24 +00:00
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END_VERSIONS
|
2021-02-12 12:00:02 +00:00
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"""
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}
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