mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
40 lines
1.1 KiB
Text
40 lines
1.1 KiB
Text
process DASTOOL_SCAFFOLDS2BIN {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' :
|
|
'quay.io/biocontainers/das_tool:1.1.3--r41hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
val(extension)
|
|
|
|
output:
|
|
tuple val(meta), path("*.tsv"), emit: scaffolds2bin
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def file_extension = extension ? extension : "fasta"
|
|
|
|
"""
|
|
gunzip -f *.${file_extension}.gz
|
|
|
|
Fasta_to_Scaffolds2Bin.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 version //' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|