mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
process DASTOOL_FASTATOCONTIG2BIN {
|
|
tag "$meta.id"
|
|
label 'process_single'
|
|
|
|
conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' :
|
|
'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
val(extension)
|
|
|
|
output:
|
|
tuple val(meta), path("*.tsv"), emit: fastatocontig2bin
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def file_extension = extension ? extension : "fasta"
|
|
def clean_fasta = fasta.toString() - ".gz"
|
|
def decompress_fasta = fasta.toString() == clean_fasta ? "" : "gunzip -q -f $fasta"
|
|
"""
|
|
$decompress_fasta
|
|
|
|
Fasta_to_Contig2Bin.sh \\
|
|
$args \\
|
|
-i . \\
|
|
-e $file_extension \\
|
|
> ${prefix}.tsv
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool //' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|