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1de4bd46b7
* Add merqury files * Remove md5sum for completeness stats file * update container and test output * Update modules/merqury/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Explicitly set thread usage for meryl * Remove empty file md5sum Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
59 lines
2.4 KiB
Text
59 lines
2.4 KiB
Text
process MERQURY {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::merqury=1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1':
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'quay.io/biocontainers/merqury:1.3--hdfd78af_1' }"
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input:
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tuple val(meta), path(meryl_db), path(assembly)
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output:
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tuple val(meta), path("*_only.bed") , emit: assembly_only_kmers_bed
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tuple val(meta), path("*_only.wig") , emit: assembly_only_kmers_wig
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tuple val(meta), path("*.completeness.stats"), emit: stats
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tuple val(meta), path("*.dist_only.hist") , emit: dist_hist
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tuple val(meta), path("*.spectra-cn.fl.png") , emit: spectra_cn_fl_png
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tuple val(meta), path("*.spectra-cn.hist") , emit: spectra_cn_hist
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tuple val(meta), path("*.spectra-cn.ln.png") , emit: spectra_cn_ln_png
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tuple val(meta), path("*.spectra-cn.st.png") , emit: spectra_cn_st_png
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tuple val(meta), path("*.spectra-asm.fl.png"), emit: spectra_asm_fl_png
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tuple val(meta), path("*.spectra-asm.hist") , emit: spectra_asm_hist
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tuple val(meta), path("*.spectra-asm.ln.png"), emit: spectra_asm_ln_png
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tuple val(meta), path("*.spectra-asm.st.png"), emit: spectra_asm_st_png
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tuple val(meta), path("${prefix}.qv") , emit: assembly_qv
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tuple val(meta), path("${prefix}.*.qv") , emit: scaffold_qv
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tuple val(meta), path("*.hist.ploidy") , emit: read_ploidy
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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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prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = 1.3
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"""
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# Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
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# Check for container variable initialisation script and source it.
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if [ -f "/usr/local/env-activate.sh" ]; then
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set +u # Otherwise, errors out because of various unbound variables
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. "/usr/local/env-activate.sh"
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set -u
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fi
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# limit meryl to use the assigned number of cores.
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export OMP_NUM_THREADS=$task.cpus
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merqury.sh \\
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$meryl_db \\
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$assembly \\
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$prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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merqury: $VERSION
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END_VERSIONS
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"""
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}
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