Then the next question is, how do we deal with the aggregation? Do we add

type: 'dna'

to the meta map or something?

//
    // Aggregate all databases for downstream processes
    //
    ch_all_databases = Channel.empty()
        .mix(
            ch_centrifuge_output.map { meta, db -> [meta + [tool: "centrifuge"], db] },
            ch_diamond_output.map { meta, db -> [meta + [tool: "diamond"], db] },
            ch_ganon_output.map { meta, db -> [meta + [tool: "ganon"], db] },
            ch_kaiju_output.map { meta, db -> [meta + [tool: "kaiju"], db] },
            ch_kraken2_bracken_output.map { meta, db -> [meta + [tool: params.build_bracken ? "bracken" : "kraken2"], db] },
            ch_krakenuniq_output.map { meta, db -> [meta + [tool: "krakenuniq"], db] },
            ch_malt_output.map { db -> [[id: params.dbname, tool: "malt"], db] },
            ch_kmcp_output.map { meta, db -> [meta + [tool: "kmcp"], db] },
            ch_sourmash_output.map { meta, db -> [meta + [tool: "sourmash"], db] },
        )

Yeah I think that's how I would do it

You're making me patch all of them, aren't you?

why would I do that

Does this make sense?

ch_all_databases = Channel.empty()
        .mix(
            ch_centrifuge_output.map { meta, db -> [meta + [tool: "centrifuge", type: 'dna'], db] },
            ch_diamond_output.map { meta, db -> [meta + [tool: "diamond", type: 'dna'], db] },
            ch_ganon_output.map { meta, db -> [meta + [tool: "ganon", type: 'dna'], db] },
            ch_kaiju_output.map { meta, db -> [meta + [tool: "kaiju", type: 'dna'], db] },
            ch_kraken2_bracken_output.map { meta, db -> [meta + [tool: params.build_bracken ? "bracken" : "kraken2", type: 'dna'], db] },
            ch_krakenuniq_output.map { meta, db -> [meta + [tool: "krakenuniq", type: 'dna'], db] },
            ch_malt_output.map { db -> [[id: params.dbname, tool: "malt", type: 'dna'], db] },
            ch_kmcp_output.map { meta, db -> [meta + [tool: "kmcp", type: 'dna'], db] },
            ch_sourmash_dna_output.map { meta, db -> [meta + [tool: 'sourmash', type: 'dna'], db] },
            ch_sourmash_protein_output.map { meta, db -> [meta + [tool: 'sourmash', type: 'protein'], db] },
        )

Yeah I think so. I would need to fix MALT but otherwise ues

Do we have any AA FASTA files for testing? Or should I create some translations?

There should be AA FASTA files in teh sheet already 🤔

I could, but then you'd be sad and I don't want that.

tenor_gif6495266977383783728.gif