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https://github.com/MillironX/nf-core_modules.git
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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
48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
def VERSION="1.0.2"
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process DEEPARG_PREDICT {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
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'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
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/*
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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).
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Original report: https://github.com/nf-core/funcscan/issues/23
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*/
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containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
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input:
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tuple val(meta), path(fasta), val(model)
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path(db)
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output:
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tuple val(meta), path("*.align.daa") , emit: daa
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tuple val(meta), path("*.align.daa.tsv") , emit: daa_tsv
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tuple val(meta), path("*.mapping.ARG") , emit: arg
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tuple val(meta), path("*.mapping.potential.ARG"), emit: potential_arg
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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deeparg \\
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predict \\
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$args \\
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-i $fasta \\
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-o ${prefix} \\
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-d $db \\
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--model $model
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deeparg: $VERSION
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END_VERSIONS
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"""
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}
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