8000 local module: peptidePrediction · Issue #96 · nf-core/epitopeprediction · GitHub
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local module: peptidePrediction #96

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marissaDubbelaar opened this issue Oct 27, 2021 · 2 comments
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local module: peptidePrediction #96

marissaDubbelaar opened this issue Oct 27, 2021 · 2 comments
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@marissaDubbelaar
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Uses epaa.py that is dependent on fred2 and mhcflurry(?)
@marissaDubbelaar marissaDubbelaar self-assigned this Oct 28, 2021
@marissaDubbelaar
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

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

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

    // Change the container
    conda (params.enable_conda ? "conda-forge::snpsift:4.2" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/snpsift:4.2--hdfd78af_5"
    } else {
        container "quay.io/biocontainers/snpsift:4.2--hdfd78af_5"
    }
    
    input:
        tuple val(meta), path(splitted_files) // combine the different paths?
    output:
        tuple val(meta), path("*.tsv"), path("*.json"), path("*.fasta"), emit predicted

    script:
        // def input_type = params.peptides ? "--peptides ${splitted_files}" : params.proteins ?  "--peptides ${splitted_files}" : "--somatic_mutations ${splitted_files}" // Add this in the groovy file
        // def ref_prot = params.proteome ? "--proteome ${params.proteome}" : "" // Add this in the groovy file
        // def wt = params.wild_type ? "--wild_type" : "" // Add this in the groovy file
        // def fasta_output = params.fasta_output ? "--fasta_output" : "" // Add this in the groovy file

        // $options.args = include ref_prot, wt, fasta_output, input_type there (finish with the input_type)


    // Is it necessary to keep software versions in, it is only used atm to include the version of syfpheiti 
    """
    epaa.py ${input_type} --identifier ${splitted_files.baseName} \
                        --alleles ${meta.alleles} \
                        --mhcclass ${params.mhc_class} \
                        --max_length ${params.max_peptide_length} \
                        --min_length ${params.min_peptide_length} \
                        --tools ${params.tools} \
                        --versions ${software_versions} \
                        --reference ${params.genome_version} \
                        $options.args ${splitted_files}
    """

}

@marissaDubbelaar marissaDubbelaar added dsl2 enhancement New feature or request labels Oct 28, 2021
@ggabernet
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Added in #124

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