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3868c3ab4b
* initial commit [ci skip] * reuse the modules code from nf-core/mag [ci skip] * add contextual information for the module [ci skip] * add stubs to avoid downloading db [ci skip] * trigger test * iterate on tests [ci skip] * itereate tests [ci skip] * add bins [ci skip] * fix stubs [ci skip] * interation on tests with stubs [ci skip] * use the existing pattern and fasta for input * accomodate the new version file format * use variable for the stub [ci skip] * update the versions file in meta.yml * Accomodate code review regarding publishDir function [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * remove extra newline * use bioconda channel * update the description for filtered file * Apply suggestions from code review * Update main.nf * Update main.nf * Update modules/gtdbtk/classifywf/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
83 lines
3.6 KiB
Text
83 lines
3.6 KiB
Text
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '1.5.0' // When using stubs for the GTDB database, the version info isn't printed.
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process GTDBTK_CLASSIFYWF {
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tag "${meta.assembler}-${meta.id}"
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0"
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} else {
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container "quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0"
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}
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input:
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tuple val(meta), path("bins/*")
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tuple val(db_name), path("database/*")
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output:
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path "gtdbtk.${meta.assembler}-${meta.id}.*.summary.tsv" , emit: summary
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path "gtdbtk.${meta.assembler}-${meta.id}.*.classify.tree.gz" , emit: tree
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path "gtdbtk.${meta.assembler}-${meta.id}.*.markers_summary.tsv", emit: markers
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path "gtdbtk.${meta.assembler}-${meta.id}.*.msa.fasta.gz" , emit: msa
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path "gtdbtk.${meta.assembler}-${meta.id}.*.user_msa.fasta" , emit: user_msa
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path "gtdbtk.${meta.assembler}-${meta.id}.*.filtered.tsv" , emit: filtered
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path "gtdbtk.${meta.assembler}-${meta.id}.log" , emit: log
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path "gtdbtk.${meta.assembler}-${meta.id}.warnings.log" , emit: warnings
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path "gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv" , emit: failed
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path "versions.yml" , emit: versions
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script:
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def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
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"""
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export GTDBTK_DATA_PATH="\${PWD}/database"
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if [ ${pplacer_scratch} != "" ] ; then
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mkdir pplacer_tmp
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fi
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gtdbtk classify_wf \\
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$options.args \\
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--genome_dir bins \\
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--prefix "gtdbtk.${meta.assembler}-${meta.id}" \\
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--out_dir "\${PWD}" \\
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--cpus $task.cpus \\
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--pplacer_cpus $params.gtdbtk_pplacer_cpus \\
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$pplacer_scratch \\
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--min_perc_aa $params.gtdbtk_min_perc_aa \\
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--min_af $params.gtdbtk_min_af
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gzip "gtdbtk.${meta.assembler}-${meta.id}".*.classify.tree "gtdbtk.${meta.assembler}-${meta.id}".*.msa.fasta
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mv gtdbtk.log "gtdbtk.${meta.assembler}-${meta.id}.log"
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mv gtdbtk.warnings.log "gtdbtk.${meta.assembler}-${meta.id}.warnings.log"
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
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END_VERSIONS
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"""
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stub:
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"""
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touch gtdbtk.${meta.assembler}-${meta.id}.stub.summary.tsv
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touch gtdbtk.${meta.assembler}-${meta.id}.stub.classify.tree.gz
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touch gtdbtk.${meta.assembler}-${meta.id}.stub.markers_summary.tsv
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touch gtdbtk.${meta.assembler}-${meta.id}.stub.msa.fasta.gz
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touch gtdbtk.${meta.assembler}-${meta.id}.stub.user_msa.fasta
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touch gtdbtk.${meta.assembler}-${meta.id}.stub.filtered.tsv
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touch gtdbtk.${meta.assembler}-${meta.id}.log
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touch gtdbtk.${meta.assembler}-${meta.id}.warnings.log
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touch gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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END_VERSIONS
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"""
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}
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