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https://github.com/MillironX/nf-core_modules.git
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6b011dd148
* Started (again) to work on bgzipping SVDB_MERGE output * Updated test yml * SVDB_MERGE now bgzips output * Fixed singularity, renamed tests in test.yml * Added samtools version Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
59 lines
1.9 KiB
Text
59 lines
1.9 KiB
Text
process SVDB_MERGE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0':
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'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0' }"
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input:
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tuple val(meta), path(vcfs)
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val (priority)
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output:
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tuple val(meta), path("*_sv_merge.vcf.gz"), emit: vcf
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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 ?: "${meta.id}"
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def input = "${vcfs.join(" ")}"
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def prio = ""
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if(priority) {
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prio = "--priority ${priority.join(',')}"
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input = ""
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for (int index = 0; index < vcfs.size(); index++) {
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input += " ${vcfs[index]}:${priority[index]}"
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}
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}
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"""
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svdb \\
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--merge \\
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$args \\
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$prio \\
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--vcf $input \\
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> ${prefix}_sv_merge.vcf
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bgzip ${prefix}_sv_merge.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
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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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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_sv_merge.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
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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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