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70 lines
2.4 KiB
Text
70 lines
2.4 KiB
Text
process MEGAHIT {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' :
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'quay.io/biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("megahit_out/*.contigs.fa.gz") , emit: contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.contigs.fa.gz") , emit: k_contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.addi.fa.gz") , emit: addi_contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.local.fa.gz") , emit: local_contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.final.contigs.fa.gz"), emit: kfinal_contigs
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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 args2 = task.ext.args2 ?: ''
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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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megahit \\
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-r ${reads} \\
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-t $task.cpus \\
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$args \\
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--out-prefix $prefix
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pigz \\
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--no-name \\
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-p $task.cpus \\
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$args2 \\
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megahit_out/*.fa \\
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megahit_out/intermediate_contigs/*.fa
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
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END_VERSIONS
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"""
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} else {
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"""
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megahit \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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-t $task.cpus \\
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$args \\
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--out-prefix $prefix
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pigz \\
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--no-name \\
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-p $task.cpus \\
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$args2 \\
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megahit_out/*.fa \\
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megahit_out/intermediate_contigs/*.fa
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
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END_VERSIONS
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"""
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}
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}
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