mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
78 lines
3.4 KiB
Text
78 lines
3.4 KiB
Text
process GTDBTK_CLASSIFYWF {
|
|
tag "${meta.assembler}-${meta.id}"
|
|
label 'process_medium'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' :
|
|
'quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path("bins/*")
|
|
tuple val(db_name), path("database/*")
|
|
|
|
output:
|
|
path "gtdbtk.${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
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
|
|
def VERSION = '1.5.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
export GTDBTK_DATA_PATH="\${PWD}/database"
|
|
if [ ${pplacer_scratch} != "" ] ; then
|
|
mkdir pplacer_tmp
|
|
fi
|
|
|
|
gtdbtk classify_wf \\
|
|
$args \\
|
|
--genome_dir bins \\
|
|
--prefix "gtdbtk.${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}-${meta.id}.warnings.log"
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gtdbtk: \$(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
|
|
"${task.process}":
|
|
gtdbtk: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|