diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf index bb9ee31fface..7061cfffbe18 100644 --- a/subworkflows/nf-core/bcl_demultiplex/main.nf +++ b/subworkflows/nf-core/bcl_demultiplex/main.nf @@ -20,6 +20,7 @@ workflow BCL_DEMULTIPLEX { ch_interop = channel.empty() ch_logs = channel.empty() ch_sav_files = channel.empty() + ch_undetermined = channel.empty() // MODULE: bclconvert // Demultiplex the bcl files @@ -28,6 +29,7 @@ workflow BCL_DEMULTIPLEX { ch_interop = ch_interop.mix(BCLCONVERT.out.interop) ch_reports = ch_reports.mix(BCLCONVERT.out.reports) ch_logs = ch_logs.mix(BCLCONVERT.out.logs) + ch_undetermined = ch_undetermined.mix(BCLCONVERT.out.undetermined) ch_sav_files = ch_sav_files.mix(BCLCONVERT.out.reports) ch_fastq_with_meta = ch_fastq_with_meta.mix( generateReadgroupBCLCONVERT( @@ -46,6 +48,7 @@ workflow BCL_DEMULTIPLEX { ch_interop = ch_interop.mix(BCL2FASTQ.out.interop) ch_reports = ch_reports.mix(BCL2FASTQ.out.reports) ch_stats = ch_stats.mix(BCL2FASTQ.out.stats) + ch_undetermined = ch_undetermined.mix(BCL2FASTQ.out.undetermined) ch_sav_files = ch_sav_files.mix(BCL2FASTQ.out.stats) ch_fastq_with_meta = ch_fastq_with_meta.mix( generateReadgroupBCL2FASTQ( @@ -83,15 +86,16 @@ workflow BCL_DEMULTIPLEX { } emit: - fastq = ch_fastq.fastq - empty_fastq = ch_fastq.empty - reports = ch_reports - stats = ch_stats - interop = ch_interop - logs = ch_logs - sav_report = MULTIQCSAV.out.report - sav_data = MULTIQCSAV.out.data - sav_plots = MULTIQCSAV.out.plots + fastq = ch_fastq.fastq + empty_fastq = ch_fastq.empty + reports = ch_reports + stats = ch_stats + interop = ch_interop + logs = ch_logs + undetermined = ch_undetermined + sav_report = MULTIQCSAV.out.report + sav_data = MULTIQCSAV.out.data + sav_plots = MULTIQCSAV.out.plots } def generateReadgroupBCLCONVERT(ch_fastq_list_csv, ch_fastq) { diff --git a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test index 7513b83a5b13..93b00c15806a 100644 --- a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test +++ b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots"]).collectEntries { key, val -> + sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots", "undetermined"]).collectEntries { key, val -> if (key == "interop") { return [ key, val.collect { meta, files -> [ @@ -93,7 +93,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots"]).collectEntries { key, val -> + sanitizeOutput(workflow.out, unstableKeys: ["empty_fastq", "logs", "sav_report", "sav_data", "sav_plots", "undetermined"]).collectEntries { key, val -> if (key == "fastq") if (key == "interop") { return [ key, val.collect { meta, files -> diff --git a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap index 5ff388d8aca6..3620536c8e42 100644 --- a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap @@ -170,14 +170,23 @@ ], "stats": [ + ], + "undetermined": [ + [ + { + "id": "HMTFYDRXX", + "lane": 1 + }, + "Undetermined_S0_L001_R1_001.fastq.gz" + ] ] } ], + "timestamp": "2026-03-16T13:47:40.083238326", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-04T19:55:51.054792" + } }, "bcl2fastq": { "content": [ @@ -309,13 +318,16 @@ "Stats.json:md5,8e5f038b8aa9e465599d3575f930e604" ] ] + ], + "undetermined": [ + ] } ], + "timestamp": "2026-03-16T13:48:09.325036018", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-04T19:42:28.852443" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_contam_seqtk_kraken/main.nf b/subworkflows/nf-core/fastq_contam_seqtk_kraken/main.nf index 1673f77a4eb6..87ea3947def7 100644 --- a/subworkflows/nf-core/fastq_contam_seqtk_kraken/main.nf +++ b/subworkflows/nf-core/fastq_contam_seqtk_kraken/main.nf @@ -39,5 +39,6 @@ workflow FASTQ_CONTAM_SEQTK_KRAKEN { ch_reports = ch_reports.mix(KRAKEN2.out.report) emit: - reports = ch_reports // channel: [ [meta], log ] + reports = ch_reports // channel: [ [meta], log ] + reads = SEQTK_SAMPLE.out.reads // channel: [ [meta], reads ] } diff --git a/subworkflows/nf-core/fastq_contam_seqtk_kraken/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_contam_seqtk_kraken/tests/main.nf.test.snap index 874616d2fdca..13f44dea0efe 100644 --- a/subworkflows/nf-core/fastq_contam_seqtk_kraken/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_contam_seqtk_kraken/tests/main.nf.test.snap @@ -20,6 +20,42 @@ "test.25000.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" ] ], + "1": [ + [ + { + "id": "test", + "single_end": true, + "n_reads": 12500 + }, + "test.12500_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ], + [ + { + "id": "test", + "single_end": true, + "n_reads": 25000 + }, + "test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true, + "n_reads": 12500 + }, + "test.12500_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ], + [ + { + "id": "test", + "single_end": true, + "n_reads": 25000 + }, + "test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], "reports": [ [ { @@ -40,11 +76,11 @@ ] } ], + "timestamp": "2026-03-16T13:43:30.024469728", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T17:23:21.150863294" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - fastq - [12500, 25000] - krakendb -- stub": { "content": [ @@ -67,6 +103,42 @@ "test.25000.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "1": [ + [ + { + "id": "test", + "single_end": true, + "n_reads": 12500 + }, + "test.12500.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ], + [ + { + "id": "test", + "single_end": true, + "n_reads": 25000 + }, + "test.25000.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true, + "n_reads": 12500 + }, + "test.12500.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ], + [ + { + "id": "test", + "single_end": true, + "n_reads": 25000 + }, + "test.25000.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], "reports": [ [ { @@ -87,14 +159,14 @@ ] }, [ - + ] ], + "timestamp": "2026-03-16T13:43:39.839595283", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T17:23:31.030729105" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - fastq - 25000 - krakendb": { "content": [ @@ -109,6 +181,26 @@ "test.25000.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" ] ], + "1": [ + [ + { + "id": "test", + "single_end": true, + "n_reads": 25000 + }, + "test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true, + "n_reads": 25000 + }, + "test.25000_test_1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], "reports": [ [ { @@ -121,10 +213,10 @@ ] } ], + "timestamp": "2026-03-16T13:43:20.617712027", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-15T17:23:10.743490624" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } -} +} \ No newline at end of file