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params.file = "example/proteins.fas"

Channel.fromPath(params.file).into{for_blast; for_signalp}

process blast_swissprot {

    input:
    file fasta from for_blast

    output:
    file "${fasta}.blast_swissprot.tsv" into blast_results

    script:
    """
    module_blast_swissprot.py --fasta $fasta > ${fasta}.blast_swissprot.tsv
    """
}

process convert_blast_swissprot {

    input:
    file result from blast_results

    output:
    file "${result}.json" into converted_blast_results

    script:
    """
    convert_blast_swissprot.py ${result} > ${result}.json
    """
}

process signalp {

    input:
    file fasta from for_signalp

    output:
    file "${fasta}.signalp.tsv" into signalp_results

    script:
    """
    module_signalp.py --fasta $fasta > ${fasta}.signalp.tsv
    """
}

process convert_signalp {

    input:
    file result from signalp_results

    output:
    file "${result}.json" into converted_signalp_results

    script:
    """
    convert_signalp.py ${result} > ${result}.json
    """
}