nf-core_modules/modules/gtdbtk/classifywf/main.nf

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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '1.5.0' // When using stubs for the GTDB database, the version info isn't printed.
process GTDBTK_CLASSIFYWF {
tag "${meta.assembler}-${meta.id}"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0"
}
input:
tuple val(meta), path("bins/*")
tuple val(db_name), path("database/*")
output:
path "gtdbtk.${meta.assembler}-${meta.id}.*.summary.tsv" , emit: summary
path "gtdbtk.${meta.assembler}-${meta.id}.*.classify.tree.gz" , emit: tree
path "gtdbtk.${meta.assembler}-${meta.id}.*.markers_summary.tsv", emit: markers
path "gtdbtk.${meta.assembler}-${meta.id}.*.msa.fasta.gz" , emit: msa
path "gtdbtk.${meta.assembler}-${meta.id}.*.user_msa.fasta" , emit: user_msa
path "gtdbtk.${meta.assembler}-${meta.id}.*.filtered.tsv" , emit: filtered
path "gtdbtk.${meta.assembler}-${meta.id}.log" , emit: log
path "gtdbtk.${meta.assembler}-${meta.id}.warnings.log" , emit: warnings
path "gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv" , emit: failed
path "versions.yml" , emit: versions
script:
def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
"""
export GTDBTK_DATA_PATH="\${PWD}/database"
if [ ${pplacer_scratch} != "" ] ; then
mkdir pplacer_tmp
fi
gtdbtk classify_wf \\
$options.args \\
--genome_dir bins \\
--prefix "gtdbtk.${meta.assembler}-${meta.id}" \\
--out_dir "\${PWD}" \\
--cpus $task.cpus \\
--pplacer_cpus $params.gtdbtk_pplacer_cpus \\
$pplacer_scratch \\
--min_perc_aa $params.gtdbtk_min_perc_aa \\
--min_af $params.gtdbtk_min_af
gzip "gtdbtk.${meta.assembler}-${meta.id}".*.classify.tree "gtdbtk.${meta.assembler}-${meta.id}".*.msa.fasta
mv gtdbtk.log "gtdbtk.${meta.assembler}-${meta.id}.log"
mv gtdbtk.warnings.log "gtdbtk.${meta.assembler}-${meta.id}.warnings.log"
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
END_VERSIONS
"""
stub:
"""
touch gtdbtk.${meta.assembler}-${meta.id}.stub.summary.tsv
touch gtdbtk.${meta.assembler}-${meta.id}.stub.classify.tree.gz
touch gtdbtk.${meta.assembler}-${meta.id}.stub.markers_summary.tsv
touch gtdbtk.${meta.assembler}-${meta.id}.stub.msa.fasta.gz
touch gtdbtk.${meta.assembler}-${meta.id}.stub.user_msa.fasta
touch gtdbtk.${meta.assembler}-${meta.id}.stub.filtered.tsv
touch gtdbtk.${meta.assembler}-${meta.id}.log
touch gtdbtk.${meta.assembler}-${meta.id}.warnings.log
touch gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo "$VERSION")
END_VERSIONS
"""
}