mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
378fa5fbb4
* initial version of gamma module * remove trailing whitespace * prettier fix * hardcode version number * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/gamma/meta.yml Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * update meta and prettier * add whitespaces * add fasta output and tests Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
def VERSION = '2.1' // Version information not provided by tool on CLI
|
|
|
|
process GAMMA {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::gamma=2.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0':
|
|
'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
path(db)
|
|
|
|
output:
|
|
tuple val(meta), path("*.gamma") , emit: gamma
|
|
tuple val(meta), path("*.psl") , emit: psl
|
|
tuple val(meta), path("*.gff") , optional:true , emit: gff
|
|
tuple val(meta), path("*.fasta"), optional:true , emit: fasta
|
|
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}"
|
|
"""
|
|
GAMMA.py \\
|
|
$args \\
|
|
$fasta \\
|
|
$db \\
|
|
$prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gamma: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|