nf-core_modules/modules/deeparg/predict/main.nf
James A. Fellows Yates f469045a95
Fix DeepARG depenency issue with singularity containers (#1397)
* fix: remove left-over unnecessary code

* Adds --fakeroot option for singularity usage with DeepARG as workaround for broken conda dependency

* Update modules/deeparg/downloaddata/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Update modules/deeparg/predict/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update main.nf

* Update main.nf

* Go back to original logic

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-03-17 13:08:51 +01:00

48 lines
1.6 KiB
Text

def VERSION="1.0.2"
process DEEPARG_PREDICT {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
container "${ 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 --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
*/
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
input:
tuple val(meta), path(fasta), val(model)
path(db)
output:
tuple val(meta), path("*.align.daa") , emit: daa
tuple val(meta), path("*.align.daa.tsv") , emit: daa_tsv
tuple val(meta), path("*.mapping.ARG") , emit: arg
tuple val(meta), path("*.mapping.potential.ARG"), emit: potential_arg
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
deeparg \\
predict \\
$args \\
-i $fasta \\
-o ${prefix} \\
-d $db \\
--model $model
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deeparg: $VERSION
END_VERSIONS
"""
}