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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>
47 lines
1.4 KiB
Text
47 lines
1.4 KiB
Text
process CHECKM_LINEAGEWF {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null)
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container "${ 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(fasta)
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val fasta_ext
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path db
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output:
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tuple val(meta), path("${prefix}") , emit: checkm_output
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tuple val(meta), path("${prefix}/lineage.ms"), emit: marker_file
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tuple val(meta), path("${prefix}.tsv") , emit: checkm_tsv
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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checkm_db = db ? "export CHECKM_DATA_PATH=${db}" : ""
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"""
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$checkm_db
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checkm \\
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lineage_wf \\
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-t $task.cpus \\
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-f ${prefix}.tsv \\
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--tab_table \\
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--pplacer_threads $task.cpus \\
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-x $fasta_ext \\
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$args \\
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. \\
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$prefix
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cat <<-END_VERSIONS > versions.yml
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"${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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