8000 local module: genPeptides · Issue #94 · nf-core/epitopeprediction · GitHub
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local module: genPeptides #94

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marissaDubbelaar opened this issue Oct 27, 2021 · 2 comments
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local module: genPeptides #94

marissaDubbelaar opened this issue Oct 27, 2021 · 2 comments
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enhancement New feature or request

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@marissaDubbelaar
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This module uses the gen_peptides.py script which is dependent on Bio.SeqIO.FastaIO (SimpleFastaParser)
and Fred2
@christopher-mohr christopher-mohr added dsl2 enhancement New feature or request labels Oct 27, 2021
@marissaDubbelaar marissaDubbelaar self-assigned this Oct 27, 2021
@marissaDubbelaar
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marissaDubbelaar commented Oct 27, 2021 •
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

params.options = [:]
options        = initOptions(params.options)

def VERSION = "2.0.7"

process GEN_PEPTIDES {

    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'', meta:[:], publish_by_meta:[]) }

    conda (params.enable_conda ? "conda-forge::fred2:2.0.7" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/fred2:2.0.7--py_0"
    } else {
        container "quay.io/biocontainers/fred2:2.0.7--py_0"
    }

    input:
        tuple val(meta)

    output:
        tuple val(meta), path("*.tsv"), emit: splitted 
    
    // when: !params.peptides // TODO: Remove this by creating a nstatement in the main workflow
    
    script:
        def prefix = options.suffix ? "${meta.sample}_${options.suffix}" : "${meta.sample}_peptides"
        
        """
        gen_peptides.py --input ${proteins} --output '${prefix}.tsv' --max_length ${params.max_peptide_length} --min_length ${params.min_peptide_length}
        cat <<-END_VERSIONS > versions.yml
            ${getProcessName(task.process)}:
                fred2: \$(echo \$VERSION )
            END_VERSIONS
        """
}

@ggabernet
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Added in #124
6751

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