Test pipeline

gistfile1.groovy

#!/usr/bin/env nextflow

statuslog = Channel.create()

genome_file = file(params.inseq)
ncrna_models = file(params.ncrna_models)
genome_chunk = Channel.fromPath(params.inseq).splitFasta( by: 3)

process predict_tRNA {
    input:
    file genome_file

    output:
    file 'aragorn.gff3' into trnas
    stdout into statuslog

    statuslog.bind("tRNA detection started")

    """
    ${params.ARAGORN_DIR}/aragorn -t ${genome_file} | grep -E -C2 '(nucleotides|Sequence)' > 1
    aragorn_to_gff3.lua < 1 > 2
    ${params.GT_DIR}/bin/gt gff3 -sort -tidy -retainids 2 > aragorn.gff3 2> /dev/null
    echo "tRNA finished"
    """
}

process cmpress {
    input:
    file ncrna_models

    output:
    file ncrna_models into pressed_model

    """
    echo ${ncrna_models}
    cmpress -F ${ncrna_models}
    """
}

process predict_ncRNA {
    input:
    file genome_chunk
    file 'models.cm' from pressed_model

    output:
    file 'cmtblouts' into cmtblouts
    stdout into statuslog

    statuslog.bind("ncRNA detection started")

    """
    cmsearch --tblout cmtblouts --cut_ga models.cm ${genome_chunk} > /dev/null
    echo "ncRNA finished"
    """
}

cmtblout = cmtblouts.collectFile()

process merge_ncrnas {
    input:
    file cmtblout

    output:
    file 'ncrna.gff3' into ncrnafile

    """
    infernal_to_gff3.lua < ${cmtblout} > 1
    ${params.GT_DIR}/bin/gt gff3 -sort -tidy -retainids 1 > ncrna.gff3
    """
}

process report {
    input:

    file 'ncrna.gff3' from ncrnafile
    file 'trna.gff3' from trnas

    output:
    stdout into result

    """
    ls -Al ncrna.gff3 trna.gff3
    """
}

result.subscribe {
    println it
}

statuslog.subscribe {
    println "log:  " + it
}