From a61f969ee704b5507e107f4a50271c9d43d3958c Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 8 Apr 2026 15:19:48 +0200 Subject: [PATCH 01/21] Added stubtest for align_bwa_bwamem2_bwameme --- .../tests/main.nf.test | 104 ++++ .../tests/main.nf.test.snap | 454 +++++++++++++++++- 2 files changed, 556 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 7e64d0355..62cfd8893 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -138,4 +138,108 @@ nextflow_workflow { } } + test("align bwamem2, stub") { + + setup { + run("BWAMEM2_INDEX") { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + restrict_to_contigs = "MT192765.1" + } + workflow { + """ + input[0] = [[:],[]] + input[1] = BWAMEM2_INDEX.out.index + input[2] = [[:],[]] + input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map + [ + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[6] = "bwamem2" + input[7] = true + input[8] = 3072 + input[9] = "illumina" + input[10] = 4 + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + } + + test("align bwameme, stub") { + + setup { + run("BWAMEME_INDEX") { + script "modules/nf-core/bwameme/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + restrict_to_contigs = "MT192765.1" + } + workflow { + """ + input[0] = [[:],[]] + input[1] = [[:],[]] + input[2] = BWAMEME_INDEX.out.index + input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map + [ + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[6] = "bwameme" + input[7] = true + input[8] = 3072 + input[9] = "illumina" + input[10] = 4 + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + } + } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 7632f79b8..abcf802fa 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -37,7 +37,457 @@ ] ] ], - "timestamp": "2026-03-13T15:04:33.885203481", + "timestamp": "2026-04-08T14:47:44.537374", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "align bwamem2, stub": { + "content": [ + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T14:48:42.172404", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "align bwameme, stub": { + "content": [ + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], 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"test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T14:49:01.39982", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -81,7 +531,7 @@ ] ] ], - "timestamp": "2026-03-13T15:05:20.75721248", + "timestamp": "2026-04-08T14:48:21.046802", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 8888e71ba405c161e053325bd737848a1163cdf5 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 8 Apr 2026 16:18:10 +0200 Subject: [PATCH 02/21] Added stubtest for align_MT --- .../local/align_MT/tests/main.nf.test | 142 ++++++ .../local/align_MT/tests/main.nf.test.snap | 422 ++++++++++++++++++ 2 files changed, 564 insertions(+) diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 5441f4256..3318b260c 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -150,4 +150,146 @@ nextflow_workflow { } } + + + test("align mt - bwamem2, stub") { + + setup { + run("BWAMEM2_INDEX", alias: 'MT_MEM2') { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'mt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + outdir = "$outputDir" + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + } + workflow { + """ + input[0] = [[:],[]] + input[1] = MT_MEM2.out.index.collect() + input[2] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[3] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + ] + ) + input[6] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + ] + ) + input[7] = "bwamem2" + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + + test("align mt - bwa, stub") { + + setup { + run("BWA_INDEX", alias: 'MT_BWA') { + script "modules/nf-core/bwa/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'mt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + outdir = "$outputDir" + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + } + workflow { + """ + input[0] = MT_BWA.out.index.collect() + input[1] = [[:],[]] + input[2] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[3] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + ] + ) + input[6] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + ] + ) + input[7] = 'bwa' + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + } diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 53cd47acd..f122b005c 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -1,4 +1,426 @@ { + "align mt - bwamem2, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T15:49:24.73309", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "align mt - bwa, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T15:51:10.749046", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "align mt - bwamem2": { "content": [ { From 6474379f045d30b085caaf911976307dc34c43e7 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 20 Apr 2026 15:24:11 +0200 Subject: [PATCH 03/21] Added stubtest for call_repeat_expansions --- .../call_repeat_expansions/tests/main.nf.test | 30 ++++ .../tests/main.nf.test.snap | 145 ++++++++++++++++++ 2 files changed, 175 insertions(+) diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 983e98df9..b708a4535 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -51,4 +51,34 @@ nextflow_workflow { } + + test("CALL_REPEAT_EXPANSIONS, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/variant_catalog.json', checkIfExists: true)).collect() + input[2] = channel.of([id:'justhusky']) + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index 58e9e8bd7..7839b9b18 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -1,4 +1,149 @@ { + "CALL_REPEAT_EXPANSIONS, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "publish": [ + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-04-20T14:48:04.074693", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "CALL_REPEAT_EXPANSIONS": { "content": [ [ From a571cd9cd2febacf8e68ca12516179efbea6056b Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 20 Apr 2026 16:44:11 +0200 Subject: [PATCH 04/21] Added the stub test for align_sentieon --- .../local/align_sentieon/tests/main.nf.test | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index b218ac4cf..3f7c79ac5 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -75,4 +75,53 @@ nextflow_workflow { } + test("align sentieon, stub") { + + setup { + run("SENTIEON_BWAINDEX") { + script "modules/nf-core/sentieon/bwaindex/main.nf" + process { + """ + input[0] = channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + aligner = "sentieon" + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + save_mapped_as_cram = true + } + workflow { + """ + input[0] = SENTIEON_BWAINDEX.out.index + input[1] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[2] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map + [ + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[4] = false + input[5] = "illumina" + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + } From 200dde09c01e41fe4a93a57642750edd30023039 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 20 Apr 2026 16:51:07 +0200 Subject: [PATCH 05/21] Updated snapshot for align_sentieon --- .../align_sentieon/tests/main.nf.test.snap | 419 +++++++++++++++++- 1 file changed, 417 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index b538612cb..b6ef91ad3 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -1,4 +1,419 @@ { + "align sentieon, stub": { + "content": [ + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "aln_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gc_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gc_summary": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "is_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mq_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "qd_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-04-20T16:45:49.119367273" + }, "align sentieon": { "content": [ [ @@ -129,10 +544,10 @@ "test_dedup.score" ] ], - "timestamp": "2026-03-14T00:02:24.597092362", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-14T00:02:24.597092362" } } \ No newline at end of file From 522fead18478e5e60d2d818392d030fe86daddf6 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Tue, 21 Apr 2026 10:47:04 +0200 Subject: [PATCH 06/21] Added stubtest for qc_bam --- subworkflows/local/qc_bam/tests/main.nf.test | 105 +++++++++++++++++++ 1 file changed, 105 insertions(+) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 184eabc40..889de7da2 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -102,6 +102,59 @@ nextflow_workflow { } + test("QC_BAM - test, bwamem2, stub") { + + options "-stub" + + when { + params { + skip_tools = null + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] + ] + ) + input[1] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[7] = channel.empty() + input[8] = channel.of('xy') + input[9] = channel.empty() + input[10] = channel.empty() + input[11] = channel.empty() + input[12] = channel.empty() + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[14] = 'wgs' + input[15] = 'bwamem2' + input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[17] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + + } + test("QC_BAM - test, sentieon") { when { @@ -182,4 +235,56 @@ nextflow_workflow { } } + test("QC_BAM - test, sentieon, stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + skip_tools = null + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] + ] + ) + input[1] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[7] = channel.empty() + input[8] = channel.of('xy') + input[9] = channel.empty() + input[10] = channel.empty() + input[11] = channel.empty() + input[12] = channel.empty() + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[14] = 'wgs' + input[15] = 'sentieon' + input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[17] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + } From ca40cb9184c3365a3bfba8e3224f1191406c38f1 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Tue, 21 Apr 2026 10:55:44 +0200 Subject: [PATCH 07/21] Added snapshot got qc_bam --- .../local/qc_bam/tests/main.nf.test.snap | 2234 ++++++++++++++++- 1 file changed, 2230 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 42f458e1c..b833f5520 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -1,4 +1,2230 @@ { + "QC_BAM - test, bwamem2, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + 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692aab7ec06e6b9a7567b04e67acd82c5eb6d7cc Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Tue, 21 Apr 2026 11:02:41 +0200 Subject: [PATCH 08/21] Revert "Added snapshot got qc_bam" This reverts commit ca40cb9184c3365a3bfba8e3224f1191406c38f1. --- .../local/qc_bam/tests/main.nf.test.snap | 2234 +---------------- 1 file changed, 4 insertions(+), 2230 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index b833f5520..42f458e1c 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -1,2230 +1,4 @@ { - "QC_BAM - test, bwamem2, stub": { - "content": [ - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - 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"earlycasualcaiman_tidditcov.wig_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], - "self_sm": [ - - ], - "sex_check": [ - - ], - "tiddit_wig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-21T10:54:33.661317026" - }, "QC_BAM - test, bwamem2": { "content": [ [ @@ -2343,11 +117,11 @@ ] ] ], + "timestamp": "2026-03-27T16:45:40.990778813", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T16:45:40.990778813" + } }, "QC_BAM - test, sentieon": { "content": [ @@ -2467,10 +241,10 @@ ] ] ], + "timestamp": "2026-03-27T17:07:36.836738984", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T17:07:36.836738984" + } } } \ No newline at end of file From 3b75c84a0a527549005cdfc5feb3669f9002b735 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 22 Apr 2026 13:36:03 +0000 Subject: [PATCH 09/21] [automated] Fix code linting --- subworkflows/local/align_MT/tests/main.nf.test | 2 +- subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test | 2 +- subworkflows/local/align_sentieon/tests/main.nf.test | 2 +- subworkflows/local/qc_bam/tests/main.nf.test | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 3318b260c..986daca5c 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -239,7 +239,7 @@ nextflow_workflow { } options "-stub" - + when { params { outdir = "$outputDir" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 62cfd8893..3a5de492a 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -207,7 +207,7 @@ nextflow_workflow { } options "-stub" - + when { params { sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 22bc04d78..5849342f3 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -91,7 +91,7 @@ nextflow_workflow { } } } - + options "-stub" when { diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 0b2559070..739c3ad18 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -226,7 +226,7 @@ nextflow_workflow { test("QC_BAM - test, sentieon, stub") { options "-stub" - + when { params { outdir = "$outputDir" From f2e9cb70af4d7543f149a67a9579a02eb3b0cf2a Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Thu, 23 Apr 2026 10:16:53 +0200 Subject: [PATCH 10/21] Added stub test for prepare_references --- .../prepare_references/tests/main.nf.test | 81 ++ .../tests/main.nf.test.snap | 1245 +++++++++++++++++ 2 files changed, 1326 insertions(+) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 56e9d6831..85dea279c 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -108,4 +108,85 @@ nextflow_workflow { } + test("Should run without failures, stub") { + + options "-stub" + + when { + params { + variant_caller = "deepvariant" + mito_name = "MT" + bait_padding = 100 + } + workflow { + """ + input[0] = "bwamem2" + input[1] = "wgs" + input[2] = null + input[3] = null + input[4] = null + input[5] = null + input[6] = params.pipelines_testdata_base_path + 'reference/reference.fasta' + input[7] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' + input[8] = null + input[9] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' + input[10] = null + input[11] = "bwa" + input[12] = null + input[13] = false + input[14] = false + input[15] = null + input[16] = null + input[17] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[18] = null + input[19] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' + input[20] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List && !sortKey.isEmpty()) { + def next = sortKey[-1] + if (next instanceof List && next.every { !(it instanceof List) }) { + // Leaf list: could be [meta, path] or [file1, file2, ...]. + // For directory outputs (e.g. BWA/BWAMEM2/HISAT2 index folders), + // nf-test represents the value as a Path at sort time rather than + // expanding it to a file list. List the directory contents to + // produce a stable, unique sort key across same-named directories. + return next.findAll { !(it instanceof Map) } + .collect { v -> + def s = v.toString() + if (s.contains(':md5,')) { + return s.split(':md5,')[0].tokenize('/').last() ?: '' + } + try { + def f = new File(s) + if (f.isDirectory()) { + return f.listFiles()?.collect { it.name }?.sort()?.join(',') ?: s.tokenize('/').last() ?: '' + } + } catch (e) {} + return s.tokenize('/').last() ?: '' + } + .sort() + .join(',') + } + sortKey = next + } + def parts = sortKey.toString().split(':md5,')[0].tokenize('/') + parts ? parts[-1] : '' + } + [name, sorted_channel] + }.sort { it[0] } + ).match() } + ) + } + + } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index ee140eaa3..49c454958 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -1,4 +1,1249 @@ { + "Should run without failures, stub": { + "content": [ + [ + [ + "0", + [ + [ + "target_bait.intervals_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "1", + [ + [ + { + "id": "dbsnp_-138-" + }, + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + ] + ] + ], + [ + "10", + [ + [ + { + "id": "reference" + }, + "reference.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "11", + [ + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "gnomad_reformated.tab.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "12", + [ + [ + { + "id": "reference" + }, + [ + "reference_mt.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + 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+ ], + "timestamp": "2026-04-23T09:48:42.84565", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ [ From 87e4407db08234b6ac9ca159ffb8d0085ec75971 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 24 Apr 2026 12:16:22 +0200 Subject: [PATCH 11/21] Updated the stub test channels to match full --- subworkflows/local/qc_bam/tests/main.nf.test | 66 ++++++++------------ 1 file changed, 27 insertions(+), 39 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 739c3ad18..3f1ac7d91 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -108,34 +108,28 @@ nextflow_workflow { workflow { """ input[0] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] - ] - ) - input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[7] = channel.empty() - input[8] = channel.of('xy') + input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[6] = channel.empty() + input[7] = channel.of('xy') + input[8] = channel.empty() input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[14] = 'wgs' - input[15] = 'bwamem2' - input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[17] = true + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[13] = 'wgs' + input[14] = 'bwamem2' + input[15] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[16] = true """ } } @@ -232,37 +226,31 @@ nextflow_workflow { outdir = "$outputDir" skip_tools = null } - workflow { + workflow { """ input[0] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] - ] - ) - input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[7] = channel.empty() - input[8] = channel.of('xy') + input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[6] = channel.empty() + input[7] = channel.of('xy') + input[8] = channel.empty() input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[14] = 'wgs' - input[15] = 'sentieon' - input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[17] = true + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[13] = 'wgs' + input[14] = 'sentieon' + input[15] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[16] = true """ } } From cf755c4bd5f93c9880b90060fefb5348bfbc9f0b Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 27 Apr 2026 15:53:41 +0200 Subject: [PATCH 12/21] Modified assertion for the sub tests and updated snapshot --- subworkflows/local/qc_bam/tests/main.nf.test | 19 ++- .../local/qc_bam/tests/main.nf.test.snap | 134 +++++++++++++++++- 2 files changed, 145 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 3f1ac7d91..0b630a835 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -137,7 +137,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ).match() + } ) } @@ -258,9 +264,14 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ).match() + } ) } - } - +} } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 42f458e1c..a13789caf 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -1,4 +1,130 @@ { + "QC_BAM - test, bwamem2, stub": { + "content": [ + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.global.dist.txt", + "earlycasualcaiman_mosdepth.per-base.bed.gz", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_mosdepth.per-base.d4", + "earlycasualcaiman_mosdepth.quantized.bed.gz", + "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "earlycasualcaiman_mosdepth.region.dist.txt", + "earlycasualcaiman_mosdepth.regions.bed.gz", + "earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "earlycasualcaiman_mosdepth.summary.txt", + "earlycasualcaiman_mosdepth.thresholds.bed.gz", + "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_tidditcov.bed", + "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png", + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-04-27T15:31:05.442602988" + }, + "QC_BAM - test, sentieon, stub": { + "content": [ + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.global.dist.txt", + "earlycasualcaiman_mosdepth.per-base.bed.gz", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_mosdepth.per-base.d4", + "earlycasualcaiman_mosdepth.quantized.bed.gz", + "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "earlycasualcaiman_mosdepth.region.dist.txt", + "earlycasualcaiman_mosdepth.regions.bed.gz", + "earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "earlycasualcaiman_mosdepth.summary.txt", + "earlycasualcaiman_mosdepth.thresholds.bed.gz", + "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_tidditcov.bed", + "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png", + "earlycasualcaiman_wgsmetrics.txt" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-04-27T15:38:50.479811008" + }, "QC_BAM - test, bwamem2": { "content": [ [ @@ -117,11 +243,11 @@ ] ] ], - "timestamp": "2026-03-27T16:45:40.990778813", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-27T16:45:40.990778813" }, "QC_BAM - test, sentieon": { "content": [ @@ -241,10 +367,10 @@ ] ] ], - "timestamp": "2026-03-27T17:07:36.836738984", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-27T17:07:36.836738984" } } \ No newline at end of file From 57532eb1a8809e9bf6cb0ae296996c8810897c7e Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Tue, 28 Apr 2026 14:20:24 +0200 Subject: [PATCH 13/21] Modified stub test for align_sentieon and added new snapshot --- .../local/align_sentieon/tests/main.nf.test | 15 +- .../align_sentieon/tests/main.nf.test.snap | 533 +++++------------- 2 files changed, 141 insertions(+), 407 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 5849342f3..b6c800a74 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -120,7 +120,20 @@ nextflow_workflow { then { assert workflow.success - assert snapshot(workflow.out).match() + assert snapshot( + workflow.out.marked_bam, + workflow.out.marked_bai, + workflow.out.aln_metrics, + workflow.out.gc_metrics, + workflow.out.gc_summary, + workflow.out.is_metrics, + workflow.out.mq_metrics, + workflow.out.qd_metrics, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ) } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index b6ef91ad3..a18f76244 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -1,418 +1,139 @@ { "align sentieon, stub": { "content": [ - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "8": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "aln_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "gc_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "gc_summary": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "is_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "mq_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "qd_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - } + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "test_dedup.bam", + "test_dedup.bam.bai", + "test_dedup.bam.metrics", + "test_dedup.bam.metrics.multiqc.tsv", + "test_dedup.score" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-20T16:45:49.119367273" + "timestamp": "2026-04-28T13:54:38.517974195" }, "align sentieon": { "content": [ From f200370c6cbf22d4cdf487440ab53734fa6979b7 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Wed, 29 Apr 2026 10:28:07 +0200 Subject: [PATCH 14/21] Fixed assertion in align_sentieon --- subworkflows/local/align_sentieon/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index b6c800a74..4aab03722 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -133,7 +133,7 @@ nextflow_workflow { .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } .collect { new File(it).name } .sort() - ) + ).match() } } From 8226075360ef4ee372095fd169ce39146df697cd Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 29 Apr 2026 13:10:11 +0200 Subject: [PATCH 15/21] Added stub test for align wes, and updated the CHANGELOG --- CHANGELOG.md | 3 +- subworkflows/local/align/tests/main.nf.test | 103 +++++++- .../local/align/tests/main.nf.test.snap | 242 +++++++++++++++++- 3 files changed, 344 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d75ef8794..f198068b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,7 +29,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] -- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) +- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807), +- Stub test for all the remaning subworkflows that were lacking it: align_bwa_bwamem2_bwameme, align_MT, align (bwameme - wes), align_sentieon, call_repeat_expansions, prepare_references, qc_bam [#820](https://github.com/nf-core/raredisease/pull/820) ### `Changed` diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 7a8e427ac..44bee596a 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -147,7 +147,7 @@ nextflow_workflow { ) } } - test("align bwamem2 - wes") { + test("align bwamem2 - wes, stub") { options "-stub" @@ -350,4 +350,105 @@ nextflow_workflow { ) } } + + + + test("align bwameme - wes, stub") { + + options "-stub" + + setup { + run("BWAMEME_INDEX", alias: 'GENOME_MEME') { + script "modules/nf-core/bwameme/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'genome'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) + ]) + """ + } + } + } + + + when { + params { + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + platform = "illumina" + min_trimmed_length = 50 + mito_name = "MT" + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.empty() + input[1] = channel.empty() + input[2] = channel.empty() + input[3] = GENOME_MEME.out.index.collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[7] = channel.fromList([ + [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + ]] + ]) + input[8] = channel.empty() + input[9] = MT_MEM2.out.index.collect() + input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = channel.empty() + input[14] = SHIFTMT_MEM2.out.index.collect() + input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[18] = true + input[19] = "bwameme" + input[20] = "wgs" + input[21] = false + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = true + input[29] = false + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort(), + workflow.out.genome_marked_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mt_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mtshift_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } + ).match() + } + ) + } + } } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index e56d30a3b..922cdc8ee 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -1,4 +1,104 @@ { + "align bwamem2 - wes, stub": { + "content": [ + [ + "earlycasualcaiman.fastp.html", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", + "earlycasualcaiman_sorted_md.cram", + "earlycasualcaiman_sorted_md.cram.crai", + "hugelymodelbat.fastp.html", + "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.log", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", + "hugelymodelbat_sorted_md.cram", + "hugelymodelbat_sorted_md.cram.crai", + "slowlycivilbuck.fastp.html", + "slowlycivilbuck.fastp.json", + "slowlycivilbuck.fastp.log", + "slowlycivilbuck_R1.fastp.fastq.gz", + "slowlycivilbuck_R2.fastp.fastq.gz", + "slowlycivilbuck_sorted_md.cram", + "slowlycivilbuck_sorted_md.cram.crai" + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_sorted_md.bam.bai" + ] + ], + [ + + ], + [ + + ], + [ + + ] + ], + "timestamp": "2026-04-29T10:49:41.402548", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "align bwamem2 - wgs": { "content": [ [ @@ -267,7 +367,7 @@ ] ] ], - "timestamp": "2026-04-14T11:13:27.943707346", + "timestamp": "2026-04-29T10:48:31.959971", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -405,7 +505,7 @@ ] ], - "timestamp": "2026-04-14T09:52:25.609505795", + "timestamp": "2026-04-29T11:06:56.369571", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -510,5 +610,143 @@ "nf-test": "0.9.4", "nextflow": "25.10.4" } + }, + "align bwameme - wes, stub": { + "content": [ + [ + "earlycasualcaiman_sorted_md.cram", + "earlycasualcaiman_sorted_md.cram.crai", + "hugelymodelbat_sorted_md.cram", + "hugelymodelbat_sorted_md.cram.crai", + "slowlycivilbuck_sorted_md.cram", + "slowlycivilbuck_sorted_md.cram.crai" + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_sorted_md.bam.bai" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck.bam.bai" + ] + ], + [ + + ] + ], + "timestamp": "2026-04-29T11:13:18.312548", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From e14a945d539bb75d2af4d755819d25cab391792a Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 29 Apr 2026 14:28:41 +0200 Subject: [PATCH 16/21] Fixed CHANGELOG with prettier --- CHANGELOG.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b337d7fb2..f1e4934e0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,14 +29,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] -<<<<<<< HEAD -- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807), -- Stub test for all the remaning subworkflows that were lacking it: align_bwa_bwamem2_bwameme, align_MT, align (bwameme - wes), align_sentieon, call_repeat_expansions, prepare_references, qc_bam [#820](https://github.com/nf-core/raredisease/pull/820) -======= + <<<<<<< HEAD +- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807), +- # Stub test for all the remaning subworkflows that were lacking it: align_bwa_bwamem2_bwameme, align_MT, align (bwameme - wes), align_sentieon, call_repeat_expansions, prepare_references, qc_bam [#820](https://github.com/nf-core/raredisease/pull/820) - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) - Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#821](https://github.com/nf-core/raredisease/pull/821) - Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823) ->>>>>>> f200370c6cbf22d4cdf487440ab53734fa6979b7 + > > > > > > > f200370c6cbf22d4cdf487440ab53734fa6979b7 ### `Changed` From 6318a7d2db8b788f16b3a8321de99a52987e7931 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Thu, 11 Jun 2026 16:15:49 +0200 Subject: [PATCH 17/21] trying to update snapshot for bwa_bwamem2_bwameme --- .../tests/main.nf.test.snap | 232 ++---------------- 1 file changed, 16 insertions(+), 216 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 15d0cd517..214750497 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -113,57 +113,7 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "4": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "marked_bai": [ + "markdup_metrics": [ [ { "groupSize": 1, @@ -175,10 +125,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "marked_bam": [ + "marked_bai": [ [ { "groupSize": 1, @@ -190,10 +140,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "metrics": [ + "marked_bam": [ [ { "groupSize": 1, @@ -205,57 +155,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "stats": [ @@ -272,9 +172,9 @@ ] } ], - "timestamp": "2026-04-08T14:48:42.172404", + "timestamp": "2026-06-11T16:06:18.512372", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -338,57 +238,7 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "4": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "marked_bai": [ + "markdup_metrics": [ [ { "groupSize": 1, @@ -400,10 +250,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "marked_bam": [ + "marked_bai": [ [ { "groupSize": 1, @@ -415,10 +265,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "metrics": [ + "marked_bam": [ [ { "groupSize": 1, @@ -430,57 +280,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "stats": [ @@ -497,9 +297,9 @@ ] } ], - "timestamp": "2026-04-08T14:49:01.39982", + "timestamp": "2026-06-11T16:06:37.969441", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, From d9ff6607f65902422965b7ca3c8f1e6174b0fd1c Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 15 Jun 2026 13:42:25 +0200 Subject: [PATCH 18/21] Modifed test and snapshot for align, and tests for qc_bam --- subworkflows/local/align/tests/main.nf.test | 13 +- .../local/align/tests/main.nf.test.snap | 720 ++++++++++++++++-- subworkflows/local/qc_bam/tests/main.nf.test | 83 +- 3 files changed, 736 insertions(+), 80 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 9d0d083e6..001e6ca7e 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -437,19 +437,20 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + { assert snapshot( + workflow.out.genome_marked_cram + .collect { meta, cramfile -> [ meta, cram(cramfile, params.pipelines_testdata_base_path + 'reference/reference.fasta').getReadsMD5() ] }, + workflow.out.genome_marked_crai + .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.mtshift_bam_bai + workflow.out.mtshift_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } + ) } } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 4d12afc3e..1975202c8 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -2,27 +2,166 @@ "align bwamem2 - wes, stub": { "content": [ [ - "earlycasualcaiman.fastp.html", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "hugelymodelbat.fastp.html", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.log", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "slowlycivilbuck.fastp.html", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md.cram.crai" + ] ], [ [ @@ -93,42 +232,283 @@ ] ], - "timestamp": "2026-04-29T10:49:41.402548", + "timestamp": "2026-06-12T15:08:42.696356", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, "align bwamem2 - wgs": { "content": [ [ - "earlycasualcaiman.fastp.html", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "earlycasualcaiman_sorted_md_primary_contigs.cram", - "earlycasualcaiman_sorted_md_primary_contigs.cram.crai", - "hugelymodelbat.fastp.html", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.log", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "hugelymodelbat_sorted_md_primary_contigs.cram", - "hugelymodelbat_sorted_md_primary_contigs.cram.crai", - "slowlycivilbuck.fastp.html", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai", - "slowlycivilbuck_sorted_md_primary_contigs.cram", - "slowlycivilbuck_sorted_md_primary_contigs.cram.crai" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.json:md5,d473c195ec66e23d39a02d4566b92d75" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat.fastp.json:md5,364c1702f8e833c70fbd36c2e0634f86" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.json:md5,7ad34e9e48159c794ce777e4e48c0b96" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d948b0bd18f6f6526f5d8832465e1542" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "bb547b29eca1afded4229826c774fc90" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "2530fd24192b09084f45011703bd4954" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "6f48b21e58c7450dd4db0bfc1268d687" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "cc1385671a27d394f628d2d7868eba80" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "e8431e5dc096f9636efd37ebfe9a5883" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md_primary_contigs.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md_primary_contigs.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md_primary_contigs.cram.crai" + ] ], [ [ @@ -367,7 +747,7 @@ ] ] ], - "timestamp": "2026-04-29T10:48:31.959971", + "timestamp": "2026-06-12T15:07:25.051508", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -606,10 +986,66 @@ ] ], [ - + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "c96587f3323ea479aebf0a8ba3ee710b", + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "9f79604c77dc54d30daff682a50399bf", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "8d810d8acecdeadc5a0e7ea159cb1343", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] ] ], - "timestamp": "2026-04-29T11:06:56.369571", + "timestamp": "2026-06-12T15:26:16.997745", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -771,12 +1207,116 @@ "align bwameme - wes, stub": { "content": [ [ - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md.cram.crai" + ] ], [ [ @@ -897,12 +1437,68 @@ ] ], [ - + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] ] ], - "timestamp": "2026-04-29T11:13:18.312548", + "timestamp": "2026-06-12T15:33:25.667453", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 4a7fa232b..3e50abfa6 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -143,13 +143,42 @@ nextflow_workflow { then { assertAll( - { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() - ).match() + workflow.out.picard_collectmultiplemetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collectmultiplemetrics_pdf + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collecthsmetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.mosdepth_global_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_summary_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_bed + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_csi + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_d4 + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_wg + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_y + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_wig + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_cov + .collect { _meta, files -> file(files).name }, + workflow.out.ucsc_wigtobigwig_bw + .collect { _meta, files -> file(files).name }, + workflow.out.chromograph_cov_plots + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.sambamba_depth_bed + .collect { _meta, files -> file(files).name }, + workflow.out.verifybamid_self_sm + .collect { _meta, files -> file(files).name }, + workflow.out.ngsbits_samplegender_tsv + .collect { _meta, files -> file(files).name } + ).match() } ) } @@ -278,13 +307,43 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() - ).match() + workflow.out.picard_collectmultiplemetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collectmultiplemetrics_pdf + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collecthsmetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.mosdepth_global_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_summary_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_bed + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_csi + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_d4 + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_wg + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_y + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_wig + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_cov + .collect { _meta, files -> file(files).name }, + workflow.out.ucsc_wigtobigwig_bw + .collect { _meta, files -> file(files).name }, + workflow.out.chromograph_cov_plots + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.sambamba_depth_bed + .collect { _meta, files -> file(files).name }, + workflow.out.verifybamid_self_sm + .collect { _meta, files -> file(files).name }, + workflow.out.ngsbits_samplegender_tsv + .collect { _meta, files -> file(files).name } + ).match() } ) } -} + } } From ff23d53dca0f7e5e0e93e79642023128d52dccb1 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 15 Jun 2026 14:19:07 +0200 Subject: [PATCH 19/21] Updated snapshot for qc_bam incl sentieon --- .../local/qc_bam/tests/main.nf.test.snap | 524 +++++++++--------- 1 file changed, 257 insertions(+), 267 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 0fafcc193..c3bab311a 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,254 +2,200 @@ "QC_BAM - test, bwamem2, stub": { "content": [ [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_mosdepth.per-base.d4", - "earlycasualcaiman_mosdepth.quantized.bed.gz", - "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "earlycasualcaiman_mosdepth.region.dist.txt", - "earlycasualcaiman_mosdepth.regions.bed.gz", - "earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "earlycasualcaiman_mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.thresholds.bed.gz", - "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bed", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov.wig_chr1.png", - "earlycasualcaiman_tidditcov.wig_chr10.png", - "earlycasualcaiman_tidditcov.wig_chr11.png", - "earlycasualcaiman_tidditcov.wig_chr12.png", - "earlycasualcaiman_tidditcov.wig_chr13.png", - "earlycasualcaiman_tidditcov.wig_chr14.png", - "earlycasualcaiman_tidditcov.wig_chr15.png", - "earlycasualcaiman_tidditcov.wig_chr16.png", - "earlycasualcaiman_tidditcov.wig_chr17.png", - "earlycasualcaiman_tidditcov.wig_chr18.png", - "earlycasualcaiman_tidditcov.wig_chr19.png", - "earlycasualcaiman_tidditcov.wig_chr2.png", - "earlycasualcaiman_tidditcov.wig_chr20.png", - "earlycasualcaiman_tidditcov.wig_chr21.png", - "earlycasualcaiman_tidditcov.wig_chr22.png", - "earlycasualcaiman_tidditcov.wig_chr3.png", - "earlycasualcaiman_tidditcov.wig_chr4.png", - "earlycasualcaiman_tidditcov.wig_chr5.png", - "earlycasualcaiman_tidditcov.wig_chr6.png", - "earlycasualcaiman_tidditcov.wig_chr7.png", - "earlycasualcaiman_tidditcov.wig_chr8.png", - "earlycasualcaiman_tidditcov.wig_chr9.png", - "earlycasualcaiman_tidditcov.wig_chrM.png", - "earlycasualcaiman_tidditcov.wig_chrX.png", - "earlycasualcaiman_tidditcov.wig_chrY.png", + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ], + [ + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" + ] + ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], + [ + "earlycasualcaiman_mosdepth.per-base.d4" + ], + [ "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ], + [ + + ], + [ + "earlycasualcaiman_tidditcov.wig" + ], + [ + "earlycasualcaiman_tidditcov.bed" + ], + [ + "earlycasualcaiman_tidditcov.bw" + ], + [ + [ + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png" + ] + ], + [ + + ], + [ + + ], + [ + ] ], + "timestamp": "2026-06-15T14:03:53.405773659", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-27T15:31:05.442602988" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "QC_BAM - test, sentieon, stub": { "content": [ [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_mosdepth.per-base.d4", - "earlycasualcaiman_mosdepth.quantized.bed.gz", - "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "earlycasualcaiman_mosdepth.region.dist.txt", - "earlycasualcaiman_mosdepth.regions.bed.gz", - "earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "earlycasualcaiman_mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.thresholds.bed.gz", - "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bed", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov.wig_chr1.png", - "earlycasualcaiman_tidditcov.wig_chr10.png", - "earlycasualcaiman_tidditcov.wig_chr11.png", - "earlycasualcaiman_tidditcov.wig_chr12.png", - "earlycasualcaiman_tidditcov.wig_chr13.png", - "earlycasualcaiman_tidditcov.wig_chr14.png", - "earlycasualcaiman_tidditcov.wig_chr15.png", - "earlycasualcaiman_tidditcov.wig_chr16.png", - "earlycasualcaiman_tidditcov.wig_chr17.png", - "earlycasualcaiman_tidditcov.wig_chr18.png", - "earlycasualcaiman_tidditcov.wig_chr19.png", - "earlycasualcaiman_tidditcov.wig_chr2.png", - "earlycasualcaiman_tidditcov.wig_chr20.png", - "earlycasualcaiman_tidditcov.wig_chr21.png", - "earlycasualcaiman_tidditcov.wig_chr22.png", - "earlycasualcaiman_tidditcov.wig_chr3.png", - "earlycasualcaiman_tidditcov.wig_chr4.png", - "earlycasualcaiman_tidditcov.wig_chr5.png", - "earlycasualcaiman_tidditcov.wig_chr6.png", - "earlycasualcaiman_tidditcov.wig_chr7.png", - "earlycasualcaiman_tidditcov.wig_chr8.png", - "earlycasualcaiman_tidditcov.wig_chr9.png", - "earlycasualcaiman_tidditcov.wig_chrM.png", - "earlycasualcaiman_tidditcov.wig_chrX.png", - "earlycasualcaiman_tidditcov.wig_chrY.png", - "earlycasualcaiman_wgsmetrics.txt" - ] - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-27T15:38:50.479811008" - }, - "QC_BAM - test, bwamem2": { - "content": [ + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov_1.png", - "earlycasualcaiman_tidditcov_10.png", - "earlycasualcaiman_tidditcov_11.png", - "earlycasualcaiman_tidditcov_12.png", - "earlycasualcaiman_tidditcov_13.png", - "earlycasualcaiman_tidditcov_14.png", - "earlycasualcaiman_tidditcov_15.png", - "earlycasualcaiman_tidditcov_16.png", - "earlycasualcaiman_tidditcov_17.png", - "earlycasualcaiman_tidditcov_18.png", - "earlycasualcaiman_tidditcov_19.png", - "earlycasualcaiman_tidditcov_2.png", - "earlycasualcaiman_tidditcov_20.png", - "earlycasualcaiman_tidditcov_21.png", - "earlycasualcaiman_tidditcov_22.png", - "earlycasualcaiman_tidditcov_3.png", - "earlycasualcaiman_tidditcov_4.png", - "earlycasualcaiman_tidditcov_5.png", - "earlycasualcaiman_tidditcov_6.png", - "earlycasualcaiman_tidditcov_7.png", - "earlycasualcaiman_tidditcov_8.png", - "earlycasualcaiman_tidditcov_9.png", - "earlycasualcaiman_tidditcov_M.png", - "earlycasualcaiman_tidditcov_X.png", - "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" + ] ], [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" ], [ - + "earlycasualcaiman_mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], + [ + "earlycasualcaiman_mosdepth.per-base.d4" + ], + [ + "earlycasualcaiman_wgsmetrics.txt" ], [ ], [ - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + "earlycasualcaiman_tidditcov.wig" ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" - ] + "earlycasualcaiman_tidditcov.bed" ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" - ] + "earlycasualcaiman_tidditcov.bw" ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png" ] + ], + [ + + ], + [ + + ], + [ + ] ], + "timestamp": "2026-06-15T14:05:39.811825004", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T16:45:40.990778813" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, - "QC_BAM - test, sentieon": { + "QC_BAM - test, bwamem2": { "content": [ [ [ @@ -288,7 +234,7 @@ ], [ - "earlycasualcaiman_wgsmetrics.txt" + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" ], [ @@ -338,67 +284,111 @@ ], [ - "earlycasualcaiman_wgsmetrics.txt" - ], + + ] + ], + "timestamp": "2026-06-15T14:02:21.833990928", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "QC_BAM - test, sentieon": { + "content": [ [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" ] ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" ] ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], + [ + + ], + [ + "earlycasualcaiman_wgsmetrics.txt" + ], + [ + + ], + [ + "earlycasualcaiman_tidditcov.wig" + ], + [ + + ], + [ + "earlycasualcaiman_tidditcov.bw" + ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + "earlycasualcaiman_tidditcov_1.png", + "earlycasualcaiman_tidditcov_10.png", + "earlycasualcaiman_tidditcov_11.png", + "earlycasualcaiman_tidditcov_12.png", + "earlycasualcaiman_tidditcov_13.png", + "earlycasualcaiman_tidditcov_14.png", + "earlycasualcaiman_tidditcov_15.png", + "earlycasualcaiman_tidditcov_16.png", + "earlycasualcaiman_tidditcov_17.png", + "earlycasualcaiman_tidditcov_18.png", + "earlycasualcaiman_tidditcov_19.png", + "earlycasualcaiman_tidditcov_2.png", + "earlycasualcaiman_tidditcov_20.png", + "earlycasualcaiman_tidditcov_21.png", + "earlycasualcaiman_tidditcov_22.png", + "earlycasualcaiman_tidditcov_3.png", + "earlycasualcaiman_tidditcov_4.png", + "earlycasualcaiman_tidditcov_5.png", + "earlycasualcaiman_tidditcov_6.png", + "earlycasualcaiman_tidditcov_7.png", + "earlycasualcaiman_tidditcov_8.png", + "earlycasualcaiman_tidditcov_9.png", + "earlycasualcaiman_tidditcov_M.png", + "earlycasualcaiman_tidditcov_X.png", + "earlycasualcaiman_tidditcov_Y.png" ] + ], + [ + + ], + [ + + ], + [ + ] ], + "timestamp": "2026-06-15T14:17:24.028920433", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T17:07:36.836738984" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file From 57bb6fd9cd680d987be51faa4683756396a16ce6 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 15 Jun 2026 14:45:01 +0200 Subject: [PATCH 20/21] Modified test and snapshot for align_sentieon --- .../local/align_sentieon/tests/main.nf.test | 36 +++++----- .../align_sentieon/tests/main.nf.test.snap | 68 +++++++++++++++---- 2 files changed, 71 insertions(+), 33 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index e776ce73c..13e208411 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -121,23 +121,23 @@ nextflow_workflow { } then { - assert workflow.success - assert snapshot( - workflow.out.marked_bam, - workflow.out.marked_bai, - workflow.out.aln_metrics, - workflow.out.gc_metrics, - workflow.out.gc_summary, - workflow.out.is_metrics, - workflow.out.mq_metrics, - workflow.out.qd_metrics, - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() - ).match() + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.marked_bai.collect { meta, baifile -> [ meta, file(baifile).name ] }, + workflow.out.aln_metrics, + workflow.out.gc_metrics, + workflow.out.gc_summary, + workflow.out.is_metrics, + workflow.out.mq_metrics, + workflow.out.qd_metrics, + workflow.out.dedup_metrics, + workflow.out.dedup_metrics_multiqc, + workflow.out.score, + ).match() + } + ) } - } - -} +} \ No newline at end of file diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index e2dc6927e..261a909f4 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -28,7 +28,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_dedup.bam.bai" ] ], [ @@ -122,18 +122,56 @@ ] ], [ - "test_dedup.bam", - "test_dedup.bam.bai", - "test_dedup.bam.metrics", - "test_dedup.bam.metrics.multiqc.tsv", - "test_dedup.score" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], + "timestamp": "2026-06-15T14:36:45.068348415", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-28T13:54:38.517974195" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "align sentieon": { "content": [ @@ -303,10 +341,10 @@ ] ] ], + "timestamp": "2026-06-15T14:42:21.699949612", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-14T00:02:24.597092362" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file From 4c85951e3f320bcfd9c36961c00c5a3898a7f263 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 15 Jun 2026 13:14:36 +0000 Subject: [PATCH 21/21] Fix pre-commit whitespace and EOF issues in subworkflow tests --- subworkflows/local/align/tests/main.nf.test | 2 +- subworkflows/local/align_sentieon/tests/main.nf.test | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 001e6ca7e..522de9632 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -450,7 +450,7 @@ nextflow_workflow { .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } - + ) } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 13e208411..e0500aa00 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -140,4 +140,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +}