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03de60e6fa
* Bump checkM version and add support for pre-defined database * Add markfile output to checkm/lineagewf and add checkm/qa * Remove unnecessary BAM from tests * Fix channels to ensure single meta * Blah * Use secondary name evwyhere * Remove second incovcatiojn * Don't run module directrly for join * And for the other test * Correct module name * Fix name again * Try and fix out_format 9 not being picked up * Contains to matches to allow regex * Fix tests (finally) * Fix verisoning * [automated] Fix linting with Prettier * Update modules/checkm/qa/main.nf Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
44 lines
1.5 KiB
Text
44 lines
1.5 KiB
Text
process CHECKM_QA {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' :
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'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file)
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path exclude_marker_file
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output:
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tuple val(meta), path("${prefix}.txt") , optional: true, emit: output
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tuple val(meta), path("${prefix}.fasta"), optional: true, emit: fasta
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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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suffix = task.ext.args?.matches(".*-o 9.*|.*--out_file 9.*") ? "fasta" : "txt"
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def coverage = coverage_file ? "--coverage_file ${coverage_file}" : ""
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def exclude = exclude_marker_file ? "--exclude_markers ${marker_filer}" : ""
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"""
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checkm \\
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qa \\
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--threads ${task.cpus} \\
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--file ${prefix}.${suffix} \\
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$marker_file \\
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$analysis_dir \\
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$coverage \\
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$exclude \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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checkm: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
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END_VERSIONS
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"""
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}
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