view resfinder/scripts/resfinder.nf @ 0:55051a9bc58d draft default tip

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#!/usr/bin/env nextflow

python3 = "python3"
resfinder = "/home/projects/cge/apps/resfinder/resfinder/run_resfinder.py"

params.indir = './'
params.ext = '.fq.gz'
params.outdir = '.'
params.species = 'other'

println("Search pattern: $params.indir*{1,2}$params.ext")

Channel
    .fromFilePairs("$params.indir*{1,2}$params.ext", followLinks: true)
    .set{ infile_ch }

process resfinder{

    cpus 5
    time '30m'
    memory '1 GB'
    clusterOptions '-V -W group_list=cge -A cge'
    executor "PBS"

    input:
    set sampleID, file(datasetFile) from infile_ch

    output:
    stdout result

    """
    set +u
    module unload mgmapper metabat fastqc
    module unload ncbi-blast perl
    source /home/projects/cge/apps/env/rf4_env/bin/activate
    module load perl
    module load ncbi-blast/2.8.1+
    if [ $params.species = 'other' ]
    then
        $python3 $resfinder -acq -ifq $datasetFile -o '$params.outdir/$sampleID' -s '$params.species'
    else
        $python3 $resfinder -acq -ifq $datasetFile -o '$params.outdir/$sampleID' -s '$params.species' --point
    fi
    """
}

/*
result.subscribe {
    println it
}
*/