I am also interested in seeing how the output val(meta), path(unclassified) etc., could be parsed to val(sample_id), path(unclassified), though I did not find them in the shared main.nf. Could you point me where this workflow is called and its output parsed?

.collectFile

preprocessed_reads
				.map { it.join(',') }
				.collectFile(name: "${workflow.runName}.csv", newLine: true)
				.set { input_kraken2 }

				input_kraken2.view { "input_kraken2: $it" }

				//split the input of kraken2 into 128 samples per batch
				input_kraken2
				.flatMap { csv_file ->
					// Read the file content and process it
					def lines = csv_file.text.split('\n').findAll { it.trim() } // Remove empty lines

					// Create batches of size 2 (batches of lines, not parsed CSV)
					def batches = lines.collate(5)

					// Return one item per batch
					return batches.withIndex().collect { batch, index ->
						def basename = csv_file.getBaseName()
						def filename = "${basename}.sub${index + 1}.csv"
						def content = batch.join('\n') + '\n'

						return [filename, content]
					}
				}
				.collectFile() { filename, content ->
					[filename, content]
				}
				.set{input_kraken2_subsets}


				input_kraken2_subsets.view { "1_subsets: $it" }

				input_kraken2_subsets
				.map{it}
				.map { it -> tuple(it, params.KRAKEN2_FILTER_DATABASE) }
								.set { input_kraken2_subsets_tuples }

				input_kraken2_subsets_tuples.view{ "2_subsets_tuples: $it" }

				KRAKEN2( input_kraken2_subsets_tuples )

				KRAKEN2.out.out_list.view { "5_kraken_out: $it" }

				KRAKEN2.out.out_list
					.collectFile(name: "${workflow.runName}.kraken2_out_all.csv", newLine: true)
					.view { "6_after_collectFile: $it" }
					.splitCsv(header: false, sep: ',', strip: true)
					.view { "7_after_splitCsv: $it" }
					.map { row -> tuple(row[0], file(row[1]), file(row[2])) }
					.view { "8_kraken2_out_list_ext: $it" }
					.set { kraken2_out_list_ext }
									//parse the list output by KRAKEN2 to again sampleID and unclas or clas pair
				kraken2_out_list_ext
				    .map { it ->
				        params.USE_KRAKEN_CLASSIFIED == "disable"
				            ? tuple(it[0], it[1])   // unclassified
				            : tuple(it[0], it[2])   // classified
				    }
				    .set { kraken_out1 }
				kraken_out1.view { "9_kraken_out1: $it" }

csv