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 """ }