mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
15c7190e22
* fix: remove left-over unnecessary code * Switch to more portable solution for singularity container issue by using bind paths * Fix input collision of dummy files * Repalce dummy with which bash * Remove dummy usage from tests * Apply suggestions from code review * Fix singularity typo
39 lines
1.2 KiB
Text
39 lines
1.2 KiB
Text
def VERSION='1.0.2'
|
|
|
|
process DEEPARG_DOWNLOADDATA {
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
|
|
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
|
|
/*
|
|
We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
|
|
Original report: https://github.com/nf-core/funcscan/issues/23
|
|
*/
|
|
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
|
|
|
|
|
|
input:
|
|
|
|
output:
|
|
path "db/" , emit: db
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
deeparg \\
|
|
download_data \\
|
|
$args \\
|
|
-o db/
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
deeparg: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|