nf-core_modules/modules/dastool/scaffolds2bin/main.nf
2022-02-04 09:53:32 +01:00

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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
"""
}