DataflowReadChannel clone(DataflowReadChannel channel) {
    // Tap
    new_ = Channel.create()
    tapped = channel.tap(new_)

    // Replace channel with tapped channel in script variables
    variables = Global.session.binding.getVariables()
    variables.each { variable, value ->
        if (value == channel) {
            variables[variable] = tapped
        }
    }

    // Return the other channel
    return new_
}

///////////////
// Input
species = Channel
    .fromPath("$params.input/species.txt")
    .splitCsv(sep: "\t", header: true)
    .map { it + [proteome: Paths.get("$params.input/proteome.${it.shortName}.fasta")] }
    .mapWithIndex { i, species -> [id: i] + species }


////////////////////////////////////////////
// Blast all vs all proteomes

// TODO
// createdb ---dbs--(tap)|--> blastp.onComplete( dbs --> deletedb )
//       --proteomes-----|

// TODO do not consume cpus
// TODO cancel run if pipeline cancels
input = clone(species)
    .map { species -> [
        species.shortName,
        species.proteome,
        "${USER}_${workflow.runName}_$species.shortName"
    ]}
process createDatabase {
    //module 'decypher'

    input:
    set speciesName, file(databaseFasta), databaseName from input

    output:
    set speciesName, databaseName into proteinDatabases

    """
    echo dc_run -parameters format_aa_into_aa -query $databaseFasta -database $databaseName -description "Temporary Cedalion database, auto-generated"
    """
}

input = clone(species)
    .map { [it.proteome, it.shortName] }
    .combine(clone(proteinDatabases))
process allVsAllProteomes {
    //module 'decypher'

    input:
    set file(fasta), species, databaseSpecies, databaseName from input

    output:
    stdout into log1

    when:
    species != databaseSpecies

    script:
    """
    echo $fasta $databaseName
    """
}
log1.view()