From e87f38d5f274d17adee87f8cb9859e1588228d84 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 20 May 2026 21:46:36 +0200 Subject: [PATCH 1/4] Reorganise tests names --- workflows/phaseimpute/tests/test_all.nf.test | 6 +- .../phaseimpute/tests/test_all.nf.test.snap | 985 +----------------- .../phaseimpute/tests/test_beagle5.nf.test | 8 +- .../tests/test_beagle5.nf.test.snap | 565 +--------- workflows/phaseimpute/tests/test_dog.nf.test | 2 +- .../phaseimpute/tests/test_dog.nf.test.snap | 2 +- .../phaseimpute/tests/test_glimpse1.nf.test | 8 +- .../tests/test_glimpse1.nf.test.snap | 884 +--------------- .../phaseimpute/tests/test_glimpse2.nf.test | 8 +- .../tests/test_glimpse2.nf.test.snap | 416 +------- .../phaseimpute/tests/test_minimac4.nf.test | 8 +- .../tests/test_minimac4.nf.test.snap | 64 +- .../phaseimpute/tests/test_panelprep.nf.test | 9 +- .../tests/test_panelprep.nf.test.snap | 116 +-- .../phaseimpute/tests/test_quilt.nf.test | 8 +- .../phaseimpute/tests/test_quilt.nf.test.snap | 679 +----------- .../phaseimpute/tests/test_quilt2.nf.test | 28 +- .../tests/test_quilt2.nf.test.snap | 284 +---- .../phaseimpute/tests/test_stitch.nf.test | 8 +- .../tests/test_stitch.nf.test.snap | 663 +----------- 20 files changed, 206 insertions(+), 4545 deletions(-) diff --git a/workflows/phaseimpute/tests/test_all.nf.test b/workflows/phaseimpute/tests/test_all.nf.test index 0c48dbe7..735f899b 100644 --- a/workflows/phaseimpute/tests/test_all.nf.test +++ b/workflows/phaseimpute/tests/test_all.nf.test @@ -8,7 +8,7 @@ nextflow_pipeline { config "./nextflow.config" - test("Check test_all - with map") { + test("Check test_all - no map - no chunks") { config "../../../conf/test_all.config" when { params { @@ -16,6 +16,7 @@ nextflow_pipeline { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" publish_all = true + map = null } } @@ -35,7 +36,7 @@ nextflow_pipeline { } } - test("Check test_all - no map") { + test("Check test_all - with map - no chunks") { config "../../../conf/test_all.config" when { params { @@ -43,7 +44,6 @@ nextflow_pipeline { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" publish_all = true - map = null } } diff --git a/workflows/phaseimpute/tests/test_all.nf.test.snap b/workflows/phaseimpute/tests/test_all.nf.test.snap index 4004054a..f2933f9c 100644 --- a/workflows/phaseimpute/tests/test_all.nf.test.snap +++ b/workflows/phaseimpute/tests/test_all.nf.test.snap @@ -1,5 +1,5 @@ { - "Check test_all - no map": { + "Check test_all - no map - no chunks": { "content": [ { "workflow size": 245, @@ -986,988 +986,7 @@ "nextflow": "26.04.0" } }, - "Check test_all": { - "content": [ - { - "workflow size": 245, - "versions": { - "ADDCOLUMNS": { - "gawk": "5.3.1" - }, - "BAMCHREXTRACT": { - "samtools": 1.23 - }, - "BCFTOOLS_ANNOTATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_CONCAT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_CONVERT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_LIGATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_PHASE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_MERGE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_MPILEUP": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_NORM": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_QUERY_TRUTH": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_STATS_PANEL": { - "bcftools": "1.23.1" - 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] - }, - { - "fileName": "simulate.csv", - "rows": [ - "sample,file,index", - "NA12878,NA12878.depth_1x.bam,NA12878.depth_1x.bam.csi", - "NA19401,NA19401.depth_1x.bam,NA19401.depth_1x.bam.csi", - "NA20359,NA20359.depth_1x.bam,NA20359.depth_1x.bam.csi" - ] - } - ] - }, - { - "all_samples.glimpse1": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - }, - "all_samples.glimpse2": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=true]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - }, - "all_samples.quilt": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=true]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - }, - "all_samples.stitch": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - } - } - ], - "timestamp": "2026-04-12T20:03:45.613944785", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, - "Check test_all - with map": { + "Check test_all - with map - no chunks": { "content": [ { "workflow size": 247, diff --git a/workflows/phaseimpute/tests/test_beagle5.nf.test b/workflows/phaseimpute/tests/test_beagle5.nf.test index c045e6d0..202559ad 100644 --- a/workflows/phaseimpute/tests/test_beagle5.nf.test +++ b/workflows/phaseimpute/tests/test_beagle5.nf.test @@ -8,13 +8,15 @@ nextflow_pipeline { config "./nextflow.config" - test("Check test_beagle5 - with chunks - with map") { + test("Check test_beagle5 - no map - no chunks") { config "../../../conf/test_beagle5.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" + chunks = null + map = null publish_all = true } } @@ -30,15 +32,13 @@ nextflow_pipeline { } } - test("Check test_beagle5 - no chunks - no map") { + test("Check test_beagle5 - with map - with chunks") { config "../../../conf/test_beagle5.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = null - map = null publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_beagle5.nf.test.snap b/workflows/phaseimpute/tests/test_beagle5.nf.test.snap index b9b05331..ea18ebb9 100644 --- a/workflows/phaseimpute/tests/test_beagle5.nf.test.snap +++ b/workflows/phaseimpute/tests/test_beagle5.nf.test.snap @@ -1,192 +1,5 @@ { - "Check test_beagle5 - without chunks": { - "content": [ - { - "workflow size": 49, - "versions": { - "BCFTOOLS_CONCAT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_LIGATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_PHASE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_QUERY_IMPUTED": { - 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test("Check test_dog - no map") { + test("Check test_dog - no map - no chunks") { config "../../../conf/test_dog.config" when { params { diff --git a/workflows/phaseimpute/tests/test_dog.nf.test.snap b/workflows/phaseimpute/tests/test_dog.nf.test.snap index 72f24807..a7a11f65 100644 --- a/workflows/phaseimpute/tests/test_dog.nf.test.snap +++ b/workflows/phaseimpute/tests/test_dog.nf.test.snap @@ -1,5 +1,5 @@ { - "Check test_dog - no map": { + "Check test_dog - no map - no chunks": { "content": [ { "workflow size": 91, diff --git a/workflows/phaseimpute/tests/test_glimpse1.nf.test b/workflows/phaseimpute/tests/test_glimpse1.nf.test index f5059215..d403d0e0 100644 --- a/workflows/phaseimpute/tests/test_glimpse1.nf.test +++ b/workflows/phaseimpute/tests/test_glimpse1.nf.test @@ -8,13 +8,15 @@ nextflow_pipeline { config "./nextflow.config" - test("Check test_glimpse1 - with chunks - with map") { + test("Check test_glimpse1 - no map - no chunks") { config "../../../conf/test.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" + chunks = null + map = null publish_all = true } } @@ -30,15 +32,13 @@ nextflow_pipeline { } } - test("Check test_glimpse1 - no chunks - no map") { + test("Check test_glimpse1 - with map - with chunks") { config "../../../conf/test.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = null - map = null publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap b/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap index dde14b51..e968e936 100644 --- a/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap +++ b/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap @@ -1,5 +1,5 @@ { - "Check test_glimpse1 - no chunks - no map": { + "Check test_glimpse1 - no map - no chunks": { "content": [ { "workflow size": 35, @@ -297,887 +297,7 @@ "nextflow": "25.10.4" } }, - "Check test_glimpse1 - with chunks - no map": { - "content": [ - { - "workflow size": 39, - "versions": { - "BAMCHREXTRACT": { - "samtools": 1.23 - 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"bcftools_stats_vqc_Count_Transitions.txt:md5,155087f472a78d07c4b2ef5a8c67089b", - "bcftools_stats_vqc_Count_Transversions.txt:md5,58b840d85196adbff10a38f210e8cd00", - "multiqc_bcftools_stats.txt:md5,333922abbf5f7e66290d034db15b370a", - "multiqc_citations.txt:md5,5cbab4ecbe14049d965fd97bd61d252b", - "multiqc_general_stats.txt:md5,835d8d185aa5146f9c88e1cc27706094" - ], - "BAM files": [ - - ], - "VCF files": [ - [ - "all_samples.batch0.glimpse1.vcf.gz", - "b158fadbefda5620a47f0c8350b8d01e" - ], - [ - "all_samples.batch0.chr21.ligate.glimpse1.vcf.gz", - "c177398366bbe151add96bc659fdaaf7" - ], - [ - "all_samples.batch0.chr22.ligate.glimpse1.vcf.gz", - "713b689c40f9e69b1ae530a339946201" - ], - [ - "NA12878.glimpse1.vcf.gz", - "5d5b32855a2fc1e3c24c628987f4db68" - ], - [ - "NA19401.glimpse1.vcf.gz", - "b170995fb1666cc55e2517b3b4ff39b3" - ], - [ - "NA20359.glimpse1.vcf.gz", - "e60d1d5b7d19b031cbe475408feeefe2" - ], - [ - "NA12878_chr21.vcf.gz", - "4198ecfcd59029b10716f2c033f96343" - ], - [ - "NA12878_chr22.vcf.gz", - "2de6a606cb5ae4284b979fc00934302f" - ], - [ - "NA19401_chr21.vcf.gz", - "307139605cffb09295b27619d1e3cf41" - ], - [ - "NA19401_chr22.vcf.gz", - "7d45992def27887e96cd859480189509" - ], - [ - "NA20359_chr21.vcf.gz", - "1cca23409d5074b28e41fcda7f978021" - ], - [ - "NA20359_chr22.vcf.gz", - "a4888d2aa2af452d115f70a58ebfb8f4" - ], - [ - "all_samples.annotate.vcf.gz", - "b9a7c83f719a9c3a3d8a39cf5f302a9d" - ], - [ - "all_samples.concat.vcf.gz", - "e6f43808fd6787f348d7614bbda9b333" - ], - [ - "all_samples_chr21.merge.vcf.gz", - "8aa42728d938b7f47130497b4dc86955" - ], - [ - "all_samples_chr22.merge.vcf.gz", - "170d05c06240dceb6f079c70b1e234e3" - ] - ], - "CSV files": [ - { - "fileName": "impute.csv", - "rows": [ - "sample,tools,file,index", - "NA12878,glimpse1,NA12878.glimpse1.vcf.gz,NA12878.glimpse1.vcf.gz.tbi", - "NA19401,glimpse1,NA19401.glimpse1.vcf.gz,NA19401.glimpse1.vcf.gz.tbi", - "NA20359,glimpse1,NA20359.glimpse1.vcf.gz,NA20359.glimpse1.vcf.gz.tbi" - ] - } - ] - }, - { - "all_samples.batch0.glimpse1": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - } - } - ], - "timestamp": "2026-05-17T14:11:31.945106119", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } - }, - "Check test_glimpse1 - with chunks - with map": { + "Check test_glimpse1 - with map - with chunks": { "content": [ { "workflow size": 41, diff --git a/workflows/phaseimpute/tests/test_glimpse2.nf.test b/workflows/phaseimpute/tests/test_glimpse2.nf.test index 2c9f2adc..7c15933b 100644 --- a/workflows/phaseimpute/tests/test_glimpse2.nf.test +++ b/workflows/phaseimpute/tests/test_glimpse2.nf.test @@ -8,13 +8,15 @@ nextflow_pipeline { config "./nextflow.config" - test("Check test_glimpse2 - with chunks - with map") { + test("Check test_glimpse2 - no map - no chunks") { config "../../../conf/test_glimpse2.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" + chunks = null + map = null publish_all = true } } @@ -30,15 +32,13 @@ nextflow_pipeline { } } - test("Check test_glimpse2 - no chunks - no map") { + test("Check test_glimpse2 - with map - with chunks") { config "../../../conf/test_glimpse2.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = null - map = null publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_glimpse2.nf.test.snap b/workflows/phaseimpute/tests/test_glimpse2.nf.test.snap index d4405847..7f584404 100644 --- a/workflows/phaseimpute/tests/test_glimpse2.nf.test.snap +++ b/workflows/phaseimpute/tests/test_glimpse2.nf.test.snap @@ -1,201 +1,11 @@ { - "Check test_glimpse2 - with chunks - no map": { + "Check test_glimpse2 - no map - no chunks": { "content": [ { - "workflow size": 28, - "versions": { - "BAMCHREXTRACT": { - "samtools": 1.23 - }, - "BCFTOOLS_CONCAT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_LIGATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_PHASE": { - 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"bcftools_stats_vqc_Count_Transversions.txt:md5,ef7a61191ad2176631e63fc5ac3a9b74", - "multiqc_bcftools_stats.txt:md5,97cf6e8503e68980e44b8db0b94fddb8", - "multiqc_citations.txt:md5,5cbab4ecbe14049d965fd97bd61d252b", - "multiqc_general_stats.txt:md5,0d145e8148487878ea5f870211ba841f" - ], - "BAM files": [ - - ], - "VCF files": [ - [ - "all_samples.batch0.glimpse2.vcf.gz", - "2c4ff9c4583dda15c5cee64a533312e5" - ], - [ - "NA12878.glimpse2.vcf.gz", - "d1177aeb8d3dcd03ec2c4e5f47405067" - ], - [ - "NA19401.glimpse2.vcf.gz", - "6c9f1d2288e4c0b0cca7dd36f5a45d54" - ], - [ - "NA20359.glimpse2.vcf.gz", - "a170c839de5c48d171475b885fa00439" - ] - ], - "CSV files": [ - { - "fileName": "impute.csv", - "rows": [ - "sample,tools,file,index", - "NA12878,glimpse2,NA12878.glimpse2.vcf.gz,NA12878.glimpse2.vcf.gz.tbi", - "NA19401,glimpse2,NA19401.glimpse2.vcf.gz,NA19401.glimpse2.vcf.gz.tbi", - "NA20359,glimpse2,NA20359.glimpse2.vcf.gz,NA20359.glimpse2.vcf.gz.tbi" - ] - } - ] - }, - { - "all_samples.batch0.glimpse2": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=true]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - } - } - ], - "timestamp": "2026-04-12T20:30:15.341468401", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, - "Check test_glimpse2 - with chunks": { - "content": [ - { - "workflow size": 28, + "workflow size": 24, "versions": { "BAMCHREXTRACT": { - "samtools": 1.23 + "samtools": "1.23" }, "BCFTOOLS_CONCAT": { "bcftools": "1.23.1" @@ -231,10 +41,10 @@ "samtools": "1.23.1" }, "TABIX_TABIX": { - "tabix": 1.21 + "tabix": "1.21" }, "VCFCHREXTRACT": { - "bcftools": 1.22 + "bcftools": "1.22" }, "Workflow": { "nf-core/phaseimpute": "v1.2.0dev" @@ -263,6 +73,10 @@ "imputation/stats/NA12878.glimpse2.bcftools_stats.txt", "imputation/stats/NA19401.glimpse2.bcftools_stats.txt", "imputation/stats/NA20359.glimpse2.bcftools_stats.txt", + "initialisation", + "initialisation/prepare_genome", + "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", + "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/bcftools-stats-subtypes.txt", @@ -319,6 +133,8 @@ "NA12878.glimpse2.bcftools_stats.txt:md5,1359dbf365ac603e1aca680f69cf716d", "NA19401.glimpse2.bcftools_stats.txt:md5,5f2daa93858e1e9697d53aaa2ac33a16", "NA20359.glimpse2.bcftools_stats.txt:md5,f89c1f7fac1ff510ecb345f8234a4e5b", + "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", + "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,9c74a2688bd333bd9c9919476514258e", "bcftools_stats_indel-lengths.txt:md5,c6e6807cefcb18f541f0f6e1c803324a", "bcftools_stats_vqc_Count_Indels.txt:md5,201aeaab7e476ca176793007dfcb9985", @@ -335,19 +151,19 @@ "VCF files": [ [ "all_samples.batch0.glimpse2.vcf.gz", - "258136e6a05acb6d361bba02bbe1f12" + "877c13b94f736af97f1eb7337403f5cc" ], [ "NA12878.glimpse2.vcf.gz", - "ec0d1259b383b77c76f65229a814bcfc" + "94e0a786ba8ea52e98c5eee7ed8d0d4d" ], [ "NA19401.glimpse2.vcf.gz", - "79e3fbd14f8541e65e1eb0f7d9edfbe7" + "896e7142a6da08e562adbeb25e4dd85a" ], [ "NA20359.glimpse2.vcf.gz", - "8350f3864ba8e8d22ed267e9758a8bcc" + "49f6f16a1dc7e612aa67a0336c80f85c" ] ], "CSV files": [ @@ -373,13 +189,13 @@ } } ], - "timestamp": "2026-04-12T20:15:24.90442267", + "timestamp": "2026-05-17T14:13:04.077268746", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.0" } }, - "Check test_glimpse2 - with chunks - with map": { + "Check test_glimpse2 - with map - with chunks": { "content": [ { "workflow size": 30, @@ -596,201 +412,5 @@ "nf-test": "0.9.5", "nextflow": "26.04.0" } - }, - "Check test_glimpse2 - no chunks - no map": { - "content": [ - { - "workflow size": 24, - "versions": { - "BAMCHREXTRACT": { - "samtools": "1.23" - }, - "BCFTOOLS_CONCAT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_LIGATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_PHASE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.23.1" - }, - "GAWK_IMPUTED": { - "gawk": "5.3.1" - }, - "GLIMPSE2_LIGATE": { - "glimpse2": "2.0.0" - }, - "GLIMPSE2_PHASE": { - "glimpse2": "2.0.0" - }, - "LISTTOFILE": { - "gawk": "5.3.1" - }, - "SAMTOOLS_FAIDX": { - "samtools": "1.23.1" - }, - "TABIX_TABIX": { - "tabix": "1.21" - }, - "VCFCHREXTRACT": { - "bcftools": "1.22" - }, - "Workflow": { - "nf-core/phaseimpute": "v1.2.0dev" - } - }, - "stable name": [ - "imputation", - "imputation/batch", - "imputation/batch/all_samples.batch0.id.txt", - "imputation/batch/all_samples.batch0.idonly.txt", - "imputation/batch/all_samples.batch0.noid.txt", - "imputation/csv", - "imputation/csv/impute.csv", - "imputation/glimpse2", - "imputation/glimpse2/concat", - "imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz", - "imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz.tbi", - "imputation/glimpse2/samples", - "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz", - "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz.tbi", - "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz", - "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz.tbi", - "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz", - "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz.tbi", - "imputation/stats", - "imputation/stats/NA12878.glimpse2.bcftools_stats.txt", - "imputation/stats/NA19401.glimpse2.bcftools_stats.txt", - "imputation/stats/NA20359.glimpse2.bcftools_stats.txt", - "initialisation", - "initialisation/prepare_genome", - "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", - "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/bcftools-stats-subtypes.txt", - "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", - "multiqc/multiqc_data/llms-full.txt", - "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc.parquet", - "multiqc/multiqc_data/multiqc_bcftools_stats.txt", - "multiqc/multiqc_data/multiqc_citations.txt", - "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_general_stats.txt", - "multiqc/multiqc_data/multiqc_software_versions.txt", - "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", - "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-cnt.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-log.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", - "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", - "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-cnt.png", - "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-log.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", - "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-cnt.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-log.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", - "multiqc/multiqc_report.html", - "pipeline_info", - "pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml" - ], - "stable path": [ - "all_samples.batch0.id.txt:md5,19595d0c2ee3d3d4e0db213e4469dac6", - "all_samples.batch0.idonly.txt:md5,b16baeecc412602ee233e14bcbe592b7", - "all_samples.batch0.noid.txt:md5,2b87699e9ed5101bc2addb7596cf16c7", - "NA12878.glimpse2.bcftools_stats.txt:md5,1359dbf365ac603e1aca680f69cf716d", - "NA19401.glimpse2.bcftools_stats.txt:md5,5f2daa93858e1e9697d53aaa2ac33a16", - "NA20359.glimpse2.bcftools_stats.txt:md5,f89c1f7fac1ff510ecb345f8234a4e5b", - "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", - "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", - "bcftools-stats-subtypes.txt:md5,9c74a2688bd333bd9c9919476514258e", - "bcftools_stats_indel-lengths.txt:md5,c6e6807cefcb18f541f0f6e1c803324a", - "bcftools_stats_vqc_Count_Indels.txt:md5,201aeaab7e476ca176793007dfcb9985", - "bcftools_stats_vqc_Count_SNP.txt:md5,8f445c0315899ebfc9dbfa13b4269693", - "bcftools_stats_vqc_Count_Transitions.txt:md5,43c2c4305e4244ed0d37bef2b64938d9", - "bcftools_stats_vqc_Count_Transversions.txt:md5,ef7a61191ad2176631e63fc5ac3a9b74", - "multiqc_bcftools_stats.txt:md5,97cf6e8503e68980e44b8db0b94fddb8", - "multiqc_citations.txt:md5,5cbab4ecbe14049d965fd97bd61d252b", - "multiqc_general_stats.txt:md5,0d145e8148487878ea5f870211ba841f" - ], - "BAM files": [ - - ], - "VCF files": [ - [ - "all_samples.batch0.glimpse2.vcf.gz", - "877c13b94f736af97f1eb7337403f5cc" - ], - [ - "NA12878.glimpse2.vcf.gz", - "94e0a786ba8ea52e98c5eee7ed8d0d4d" - ], - [ - "NA19401.glimpse2.vcf.gz", - "896e7142a6da08e562adbeb25e4dd85a" - ], - [ - "NA20359.glimpse2.vcf.gz", - "49f6f16a1dc7e612aa67a0336c80f85c" - ] - ], - "CSV files": [ - { - "fileName": "impute.csv", - "rows": [ - "sample,tools,file,index", - "NA12878,glimpse2,NA12878.glimpse2.vcf.gz,NA12878.glimpse2.vcf.gz.tbi", - "NA19401,glimpse2,NA19401.glimpse2.vcf.gz,NA19401.glimpse2.vcf.gz.tbi", - "NA20359,glimpse2,NA20359.glimpse2.vcf.gz,NA20359.glimpse2.vcf.gz.tbi" - ] - } - ] - }, - { - "all_samples.batch0.glimpse2": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=true]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - } - } - ], - "timestamp": "2026-05-17T14:13:04.077268746", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } } } \ No newline at end of file diff --git a/workflows/phaseimpute/tests/test_minimac4.nf.test b/workflows/phaseimpute/tests/test_minimac4.nf.test index 90ff5642..6bc3ddb6 100644 --- a/workflows/phaseimpute/tests/test_minimac4.nf.test +++ b/workflows/phaseimpute/tests/test_minimac4.nf.test @@ -8,13 +8,15 @@ nextflow_pipeline { config "./nextflow.config" - test("Check test_minimac4 - with chunks - with map") { + test("Check test_minimac4 - no map - no chunks") { config "../../../conf/test_minimac4.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" + chunks = null + map = null publish_all = true } } @@ -30,15 +32,13 @@ nextflow_pipeline { } } - test("Check test_minimac4 - no chunks - no map") { + test("Check test_minimac4 - with map - with chunks") { config "../../../conf/test_minimac4.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = null - map = null publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_minimac4.nf.test.snap b/workflows/phaseimpute/tests/test_minimac4.nf.test.snap index 1186a963..d07e1ba2 100644 --- a/workflows/phaseimpute/tests/test_minimac4.nf.test.snap +++ b/workflows/phaseimpute/tests/test_minimac4.nf.test.snap @@ -1,8 +1,8 @@ { - "Check test_minimac4 - with chunks - with map": { + "Check test_minimac4 - no map - no chunks": { "content": [ { - "workflow size": 65, + "workflow size": 63, "versions": { "BCFTOOLS_CONCAT": { "bcftools": "1.23.1" @@ -22,11 +22,6 @@ "BCFTOOLS_STATS_TOOLS": { "bcftools": "1.23.1" }, - "CUSTOM_GENETICMAPCONVERT": { - "r-base": "4.5.3", - "r-data.table": "1.17.8", - "r-janitor": "2.2.1" - }, "GAWK_IMPUTED": { "gawk": "5.3.1" }, @@ -76,15 +71,6 @@ "imputation/stats/NA19401.minimac4.bcftools_stats.txt", "imputation/stats/NA20359.minimac4.bcftools_stats.txt", "initialisation", - "initialisation/map_convertion", - "initialisation/map_convertion/1000GP_chr21.glimpse.map", - "initialisation/map_convertion/1000GP_chr21.minimac.map", - "initialisation/map_convertion/1000GP_chr21.plink.map", - "initialisation/map_convertion/1000GP_chr21.stitch.map", - "initialisation/map_convertion/1000GP_chr22.glimpse.map", - "initialisation/map_convertion/1000GP_chr22.minimac.map", - "initialisation/map_convertion/1000GP_chr22.plink.map", - "initialisation/map_convertion/1000GP_chr22.stitch.map", "initialisation/prepare_genome", "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", @@ -141,14 +127,6 @@ "NA12878.minimac4.bcftools_stats.txt:md5,5af867d3d54f3cdbc9dfcb5e7e651449", "NA19401.minimac4.bcftools_stats.txt:md5,5b3b724bced2bed3b1c5f646cfaa9f92", "NA20359.minimac4.bcftools_stats.txt:md5,7b0580f0a386be26e33e724b18647d03", - "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", - "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", - "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", - "1000GP_chr21.stitch.map:md5,939930334691cc1730c3c322af8c2c32", - "1000GP_chr22.glimpse.map:md5,d541ba3ef55d3cff7ad3273ba4be7c64", - "1000GP_chr22.minimac.map:md5,1e35445b12cf8dfb1273500223a43a70", - "1000GP_chr22.plink.map:md5,b70cfdef56d870e575ab29374cfcecd3", - "1000GP_chr22.stitch.map:md5,24eea1320e0033b04c5f5e6fb7cff690", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,a6ea6fbba2fab0d9899174bee8f9c68f", @@ -175,7 +153,7 @@ ], [ "NA20359.minimac4.vcf.gz", - "6ad4d1a1650167306170429c6e05d53a" + "fe1e4594889ac1a353fb93ab8268ac6b" ], [ "NA12878.minimac4.vcf.gz", @@ -187,7 +165,7 @@ ], [ "NA20359.minimac4.vcf.gz", - "6ad4d1a1650167306170429c6e05d53a" + "fe1e4594889ac1a353fb93ab8268ac6b" ] ], "CSV files": [ @@ -211,16 +189,16 @@ } } ], - "timestamp": "2026-05-17T15:40:08.659438195", + "timestamp": "2026-05-17T14:15:21.729409654", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" } }, - "Check test_minimac4 - no chunks - no map": { + "Check test_minimac4 - with map - with chunks": { "content": [ { - "workflow size": 63, + "workflow size": 65, "versions": { "BCFTOOLS_CONCAT": { "bcftools": "1.23.1" @@ -240,6 +218,11 @@ "BCFTOOLS_STATS_TOOLS": { "bcftools": "1.23.1" }, + "CUSTOM_GENETICMAPCONVERT": { + "r-base": "4.5.3", + "r-data.table": "1.17.8", + "r-janitor": "2.2.1" + }, "GAWK_IMPUTED": { "gawk": "5.3.1" }, @@ -289,6 +272,15 @@ "imputation/stats/NA19401.minimac4.bcftools_stats.txt", "imputation/stats/NA20359.minimac4.bcftools_stats.txt", "initialisation", + "initialisation/map_convertion", + "initialisation/map_convertion/1000GP_chr21.glimpse.map", + "initialisation/map_convertion/1000GP_chr21.minimac.map", + "initialisation/map_convertion/1000GP_chr21.plink.map", + "initialisation/map_convertion/1000GP_chr21.stitch.map", + "initialisation/map_convertion/1000GP_chr22.glimpse.map", + "initialisation/map_convertion/1000GP_chr22.minimac.map", + "initialisation/map_convertion/1000GP_chr22.plink.map", + "initialisation/map_convertion/1000GP_chr22.stitch.map", "initialisation/prepare_genome", "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", @@ -345,6 +337,14 @@ "NA12878.minimac4.bcftools_stats.txt:md5,5af867d3d54f3cdbc9dfcb5e7e651449", "NA19401.minimac4.bcftools_stats.txt:md5,5b3b724bced2bed3b1c5f646cfaa9f92", "NA20359.minimac4.bcftools_stats.txt:md5,7b0580f0a386be26e33e724b18647d03", + "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", + "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", + "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", + "1000GP_chr21.stitch.map:md5,939930334691cc1730c3c322af8c2c32", + "1000GP_chr22.glimpse.map:md5,d541ba3ef55d3cff7ad3273ba4be7c64", + "1000GP_chr22.minimac.map:md5,1e35445b12cf8dfb1273500223a43a70", + "1000GP_chr22.plink.map:md5,b70cfdef56d870e575ab29374cfcecd3", + "1000GP_chr22.stitch.map:md5,24eea1320e0033b04c5f5e6fb7cff690", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,a6ea6fbba2fab0d9899174bee8f9c68f", @@ -371,7 +371,7 @@ ], [ "NA20359.minimac4.vcf.gz", - "fe1e4594889ac1a353fb93ab8268ac6b" + "6ad4d1a1650167306170429c6e05d53a" ], [ "NA12878.minimac4.vcf.gz", @@ -383,7 +383,7 @@ ], [ "NA20359.minimac4.vcf.gz", - "fe1e4594889ac1a353fb93ab8268ac6b" + "6ad4d1a1650167306170429c6e05d53a" ] ], "CSV files": [ @@ -407,7 +407,7 @@ } } ], - "timestamp": "2026-05-17T14:15:21.729409654", + "timestamp": "2026-05-17T15:40:08.659438195", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/phaseimpute/tests/test_panelprep.nf.test b/workflows/phaseimpute/tests/test_panelprep.nf.test index 6e3240c0..df8c8dd8 100644 --- a/workflows/phaseimpute/tests/test_panelprep.nf.test +++ b/workflows/phaseimpute/tests/test_panelprep.nf.test @@ -8,15 +8,14 @@ nextflow_pipeline { config "./nextflow.config" - - test("Check test_panelprep - with chunks - with map") { + test("Check test_panelprep - no map - no chunks") { config "../../../conf/test_panelprep.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = "${projectDir}/tests/csv/chunks.csv" + map = null publish_all = true } } @@ -31,14 +30,14 @@ nextflow_pipeline { } } - test("Check test_panelprep - no chunks - no map") { + test("Check test_panelprep - with map - with chunks") { config "../../../conf/test_panelprep.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - map = null + chunks = "${projectDir}/tests/csv/chunks.csv" publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_panelprep.nf.test.snap b/workflows/phaseimpute/tests/test_panelprep.nf.test.snap index 3f79c482..56e66013 100644 --- a/workflows/phaseimpute/tests/test_panelprep.nf.test.snap +++ b/workflows/phaseimpute/tests/test_panelprep.nf.test.snap @@ -1,8 +1,8 @@ { - "Check test_panelprep - with chunks - with map": { + "Check test_panelprep - no map - no chunks": { "content": [ { - "workflow size": 34, + "workflow size": 36, "versions": { "BCFTOOLS_CONVERT": { "bcftools": "1.23.1" @@ -22,14 +22,15 @@ "BCFTOOLS_VIEW": { "bcftools": "1.23.1" }, - "CUSTOM_GENETICMAPCONVERT": { - "r-base": "4.5.3", - "r-data.table": "1.17.8", - "r-janitor": "2.2.1" - }, "GAWK": { "gawk": "5.3.1" }, + "GLIMPSE2_CHUNK": { + "glimpse2": "2.0.0" + }, + "GLIMPSE_CHUNK": { + "glimpse": "1.1.1" + }, "SAMTOOLS_FAIDX": { "samtools": "1.23.1" }, @@ -54,15 +55,6 @@ }, "stable name": [ "initialisation", - "initialisation/map_convertion", - "initialisation/map_convertion/1000GP_chr21.glimpse.map", - "initialisation/map_convertion/1000GP_chr21.minimac.map", - "initialisation/map_convertion/1000GP_chr21.plink.map", - "initialisation/map_convertion/1000GP_chr21.stitch.map", - "initialisation/map_convertion/1000GP_chr22.glimpse.map", - "initialisation/map_convertion/1000GP_chr22.minimac.map", - "initialisation/map_convertion/1000GP_chr22.plink.map", - "initialisation/map_convertion/1000GP_chr22.stitch.map", "initialisation/prepare_genome", "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", @@ -79,7 +71,15 @@ "pipeline_info", "pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml", "prep_panel", + "prep_panel/chunks", + "prep_panel/chunks/glimpse1", + "prep_panel/chunks/glimpse1/1000GP_chr21_chunks_glimpse1.txt", + "prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt", + "prep_panel/chunks/glimpse2", + "prep_panel/chunks/glimpse2/1000GP_chr21_chunks_glimpse2.txt", + "prep_panel/chunks/glimpse2/1000GP_chr22_chunks_glimpse2.txt", "prep_panel/csv", + "prep_panel/csv/chunks_glimpse1.csv", "prep_panel/csv/panel.csv", "prep_panel/csv/posfile.csv", "prep_panel/haplegend", @@ -126,17 +126,13 @@ "prep_panel/sites/1000GP_chr22_glimpse1_sites.vcf.gz.tbi" ], "stable path": [ - "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", - "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", - "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", - "1000GP_chr21.stitch.map:md5,939930334691cc1730c3c322af8c2c32", - "1000GP_chr22.glimpse.map:md5,d541ba3ef55d3cff7ad3273ba4be7c64", - "1000GP_chr22.minimac.map:md5,1e35445b12cf8dfb1273500223a43a70", - "1000GP_chr22.plink.map:md5,b70cfdef56d870e575ab29374cfcecd3", - "1000GP_chr22.stitch.map:md5,24eea1320e0033b04c5f5e6fb7cff690", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "1000GP_chr21_chunks_glimpse1.txt:md5,64ca4a1655363e4a4e558836e5ac12f9", + "1000GP_chr22_chunks_glimpse1.txt:md5,3344e171251722cf58ae31136da223ac", + "1000GP_chr21_chunks_glimpse2.txt:md5,834dea86a63b5a49d36f53c0ac7e01a2", + "1000GP_chr22_chunks_glimpse2.txt:md5,c363e235162ca0f7d22e5604c192e256", "1000GP_chr21.hap.gz:md5,64d7fdfc96ce79848cf9c3c220e6774f", "1000GP_chr21.legend.gz:md5,3f7edc4c153521a0871c9d51f7da2372", "1000GP_chr21.samples:md5,d8ca3e8336976001de8df6be7ae236cb", @@ -166,7 +162,7 @@ ], [ "1000GP_chr21_phased.vcf.gz", - "c848bc7161431a962bc9d08c7b009e65" + "797b0fd345ce761987d4b3bddac4236a" ], [ "1000GP_chr22_fixup.vcf.gz", @@ -182,7 +178,7 @@ ], [ "1000GP_chr22_phased.vcf.gz", - "791ca241f3cd9b868a2d4492d3062f57" + "b489f8697dda10f5e2eafaa7053bd494" ], [ "1000GP_chr21_glimpse1_sites.vcf.gz", @@ -194,6 +190,14 @@ ] ], "CSV files": [ + { + "fileName": "chunks_glimpse1.csv", + "rows": [ + "panel,chr,file", + "1000GP,chr21,1000GP_chr21_chunks_glimpse1.txt", + "1000GP,chr22,1000GP_chr22_chunks_glimpse1.txt" + ] + }, { "fileName": "panel.csv", "rows": [ @@ -213,16 +217,16 @@ ] } ], - "timestamp": "2026-05-17T15:42:03.129095578", + "timestamp": "2026-05-17T14:17:12.552259413", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" } }, - "Check test_panelprep - no chunks - no map": { + "Check test_panelprep - with map - with chunks": { "content": [ { - "workflow size": 36, + "workflow size": 34, "versions": { "BCFTOOLS_CONVERT": { "bcftools": "1.23.1" @@ -242,15 +246,14 @@ "BCFTOOLS_VIEW": { "bcftools": "1.23.1" }, + "CUSTOM_GENETICMAPCONVERT": { + "r-base": "4.5.3", + "r-data.table": "1.17.8", + "r-janitor": "2.2.1" + }, "GAWK": { "gawk": "5.3.1" }, - "GLIMPSE2_CHUNK": { - "glimpse2": "2.0.0" - }, - "GLIMPSE_CHUNK": { - "glimpse": "1.1.1" - }, "SAMTOOLS_FAIDX": { "samtools": "1.23.1" }, @@ -275,6 +278,15 @@ }, "stable name": [ "initialisation", + "initialisation/map_convertion", + "initialisation/map_convertion/1000GP_chr21.glimpse.map", + "initialisation/map_convertion/1000GP_chr21.minimac.map", + "initialisation/map_convertion/1000GP_chr21.plink.map", + "initialisation/map_convertion/1000GP_chr21.stitch.map", + "initialisation/map_convertion/1000GP_chr22.glimpse.map", + "initialisation/map_convertion/1000GP_chr22.minimac.map", + "initialisation/map_convertion/1000GP_chr22.plink.map", + "initialisation/map_convertion/1000GP_chr22.stitch.map", "initialisation/prepare_genome", "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", @@ -291,15 +303,7 @@ "pipeline_info", "pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml", "prep_panel", - "prep_panel/chunks", - "prep_panel/chunks/glimpse1", - "prep_panel/chunks/glimpse1/1000GP_chr21_chunks_glimpse1.txt", - "prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt", - "prep_panel/chunks/glimpse2", - "prep_panel/chunks/glimpse2/1000GP_chr21_chunks_glimpse2.txt", - "prep_panel/chunks/glimpse2/1000GP_chr22_chunks_glimpse2.txt", "prep_panel/csv", - "prep_panel/csv/chunks_glimpse1.csv", "prep_panel/csv/panel.csv", "prep_panel/csv/posfile.csv", "prep_panel/haplegend", @@ -346,13 +350,17 @@ "prep_panel/sites/1000GP_chr22_glimpse1_sites.vcf.gz.tbi" ], "stable path": [ + "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", + "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", + "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", + "1000GP_chr21.stitch.map:md5,939930334691cc1730c3c322af8c2c32", + "1000GP_chr22.glimpse.map:md5,d541ba3ef55d3cff7ad3273ba4be7c64", + "1000GP_chr22.minimac.map:md5,1e35445b12cf8dfb1273500223a43a70", + "1000GP_chr22.plink.map:md5,b70cfdef56d870e575ab29374cfcecd3", + "1000GP_chr22.stitch.map:md5,24eea1320e0033b04c5f5e6fb7cff690", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "1000GP_chr21_chunks_glimpse1.txt:md5,64ca4a1655363e4a4e558836e5ac12f9", - "1000GP_chr22_chunks_glimpse1.txt:md5,3344e171251722cf58ae31136da223ac", - "1000GP_chr21_chunks_glimpse2.txt:md5,834dea86a63b5a49d36f53c0ac7e01a2", - "1000GP_chr22_chunks_glimpse2.txt:md5,c363e235162ca0f7d22e5604c192e256", "1000GP_chr21.hap.gz:md5,64d7fdfc96ce79848cf9c3c220e6774f", "1000GP_chr21.legend.gz:md5,3f7edc4c153521a0871c9d51f7da2372", "1000GP_chr21.samples:md5,d8ca3e8336976001de8df6be7ae236cb", @@ -382,7 +390,7 @@ ], [ "1000GP_chr21_phased.vcf.gz", - "797b0fd345ce761987d4b3bddac4236a" + "c848bc7161431a962bc9d08c7b009e65" ], [ "1000GP_chr22_fixup.vcf.gz", @@ -398,7 +406,7 @@ ], [ "1000GP_chr22_phased.vcf.gz", - "b489f8697dda10f5e2eafaa7053bd494" + "791ca241f3cd9b868a2d4492d3062f57" ], [ "1000GP_chr21_glimpse1_sites.vcf.gz", @@ -410,14 +418,6 @@ ] ], "CSV files": [ - { - "fileName": "chunks_glimpse1.csv", - "rows": [ - "panel,chr,file", - "1000GP,chr21,1000GP_chr21_chunks_glimpse1.txt", - "1000GP,chr22,1000GP_chr22_chunks_glimpse1.txt" - ] - }, { "fileName": "panel.csv", "rows": [ @@ -437,7 +437,7 @@ ] } ], - "timestamp": "2026-05-17T14:17:12.552259413", + "timestamp": "2026-05-17T15:42:03.129095578", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/workflows/phaseimpute/tests/test_quilt.nf.test b/workflows/phaseimpute/tests/test_quilt.nf.test index f2c73f30..817b869e 100644 --- a/workflows/phaseimpute/tests/test_quilt.nf.test +++ b/workflows/phaseimpute/tests/test_quilt.nf.test @@ -9,13 +9,15 @@ nextflow_pipeline { config "./nextflow.config" - test("Check test_quilt - with chunks - with map") { + test("Check test_quilt - no map - no chunks") { config "../../../conf/test_quilt.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" + chunks = null + map = null publish_all = true } } @@ -31,15 +33,13 @@ nextflow_pipeline { } } - test("Check test_quilt - no chunks - no map") { + test("Check test_quilt - with map - with chunks") { config "../../../conf/test_quilt.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = null - map = null publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_quilt.nf.test.snap b/workflows/phaseimpute/tests/test_quilt.nf.test.snap index fc59977a..9a63f01c 100644 --- a/workflows/phaseimpute/tests/test_quilt.nf.test.snap +++ b/workflows/phaseimpute/tests/test_quilt.nf.test.snap @@ -1,680 +1,5 @@ { - "Check test_quilt - without chunks": { - "content": [ - { - "workflow size": 24, - "versions": { - "BAMCHREXTRACT": { - "samtools": 1.23 - }, - "BCFTOOLS_CONCAT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.23.1" - }, - 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test("Check test_quilt2 - with chunks - with map") { - config "../../../conf/test_quilt2.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.quilt2": UTILS.vcfDetails("$outputDir/imputation/quilt2/concat/all_samples.batch0.quilt2.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_quilt2 - with chunks - no map") { + test("Check test_quilt2 - no map - no chunks") { config "../../../conf/test_quilt2.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" + chunks = null map = null publish_all = true } @@ -54,14 +33,13 @@ nextflow_pipeline { } } - test("Check test_quilt2 - no chunks - with map") { + test("Check test_quilt2 - with map - with chunks") { config "../../../conf/test_quilt2.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = null publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_quilt2.nf.test.snap b/workflows/phaseimpute/tests/test_quilt2.nf.test.snap index 897f2e0a..841f23a1 100644 --- a/workflows/phaseimpute/tests/test_quilt2.nf.test.snap +++ b/workflows/phaseimpute/tests/test_quilt2.nf.test.snap @@ -1,8 +1,8 @@ { - "Check test_quilt2 - with chunks - no map": { + "Check test_quilt2 - no map - no chunks": { "content": [ { - "workflow size": 24, + "workflow size": 22, "versions": { "BAMCHREXTRACT": { "samtools": "1.23" @@ -48,243 +48,6 @@ "nf-core/phaseimpute": "v1.2.0dev" } }, - "stable name": [ - "imputation", - "imputation/batch", - "imputation/batch/all_samples.batch0.id.txt", - 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}, - "GAWK_IMPUTED": { - "gawk": "5.3.1" - }, - "GLIMPSE2_LIGATE": { - "glimpse2": "2.0.0" - }, - "LISTTOFILE": { - "gawk": "5.3.1" - }, - "QUILT_QUILT2": { - "r-base": "4.4.3", - "r-quilt": "2.0.4" - }, - "SAMTOOLS_FAIDX": { - "samtools": "1.23.1" - }, - "TABIX_TABIX": { - "tabix": "1.21" - }, - "VCFCHREXTRACT": { - "bcftools": "1.22" - }, - "Workflow": { - "nf-core/phaseimpute": "v1.2.0dev" - } - }, "stable name": [ "imputation", "imputation/batch", @@ -319,15 +82,6 @@ "imputation/stats/NA19401.quilt2.bcftools_stats.txt", "imputation/stats/NA20359.quilt2.bcftools_stats.txt", "initialisation", - "initialisation/map_convertion", - "initialisation/map_convertion/1000GP_chr21.glimpse.map", - "initialisation/map_convertion/1000GP_chr21.minimac.map", - "initialisation/map_convertion/1000GP_chr21.plink.map", - "initialisation/map_convertion/1000GP_chr21.stitch.map", - "initialisation/map_convertion/1000GP_chr22.glimpse.map", - "initialisation/map_convertion/1000GP_chr22.minimac.map", - "initialisation/map_convertion/1000GP_chr22.plink.map", - "initialisation/map_convertion/1000GP_chr22.stitch.map", "initialisation/prepare_genome", "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", @@ -387,14 +141,6 @@ "NA12878.quilt2.bcftools_stats.txt:md5,764240dc8d060a232cc2f9e1d048a3fb", "NA19401.quilt2.bcftools_stats.txt:md5,319fec13929c123e74dac0db2186b468", "NA20359.quilt2.bcftools_stats.txt:md5,593343e7b2ae9b51bc7774095c6cb0da", - "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", - "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", - "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", - "1000GP_chr21.stitch.map:md5,939930334691cc1730c3c322af8c2c32", - "1000GP_chr22.glimpse.map:md5,d541ba3ef55d3cff7ad3273ba4be7c64", - "1000GP_chr22.minimac.map:md5,1e35445b12cf8dfb1273500223a43a70", - "1000GP_chr22.plink.map:md5,b70cfdef56d870e575ab29374cfcecd3", - "1000GP_chr22.stitch.map:md5,24eea1320e0033b04c5f5e6fb7cff690", "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,46f8e72c54af931bec43d50346e6c245", @@ -413,19 +159,19 @@ "VCF files": [ [ "all_samples.batch0.quilt2.vcf.gz", - "5585090528c5cd4a028733d7594e4284" + "2fee7e17d0f94516684e69c9ad852524" ], [ "NA12878.quilt2.vcf.gz", - "c491e0822babc104a38e21d2ababdbcc" + "5b24356dcf66789c9131ab0ec571dcc2" ], [ "NA19401.quilt2.vcf.gz", - "d7ec86f857fe49917e19286c84d53fe1" + "c3ca81440ada4d0dea1d52274b668f93" ], [ "NA20359.quilt2.vcf.gz", - "679d3a09495d87789363c86e7c05092d" + "f1a8b0d39b3fe5648428c7a35b87d97f" ], [ "all_samples.batch0.chr21.quilt2.ligate.vcf.gz", @@ -437,11 +183,11 @@ ], [ "all_samples.batch0.chr22.quilt2.ligate.vcf.gz", - "328ad6f108ee9b95dd355ce6c4069acf" + "63843cb986b001f6d7a24124f8a43570" ], [ "all_samples.batch0.chr22_16570000-16610000.quilt2.vcf.gz", - "857a9ea039ac3184a8ba006f695e6a9f" + "2208d7384aec1559c946df908c8ec0a6" ] ], "CSV files": [ @@ -467,13 +213,13 @@ } } ], - "timestamp": "2026-05-19T16:11:28.782157639", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } + "nf-test": "0.9.3", + "nextflow": "26.04.1" + }, + "timestamp": "2026-05-20T17:59:50.817250158" }, - "Check test_quilt2 - with chunks - with map": { + "Check test_quilt2 - with map - with chunks": { "content": [ { "workflow size": 26, @@ -721,10 +467,10 @@ } } ], - "timestamp": "2026-05-19T16:08:39.594192642", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" - } + }, + "timestamp": "2026-05-19T16:08:39.594192642" } } \ No newline at end of file diff --git a/workflows/phaseimpute/tests/test_stitch.nf.test b/workflows/phaseimpute/tests/test_stitch.nf.test index f9c07496..b559db47 100644 --- a/workflows/phaseimpute/tests/test_stitch.nf.test +++ b/workflows/phaseimpute/tests/test_stitch.nf.test @@ -9,13 +9,15 @@ nextflow_pipeline { config "./nextflow.config" - test("Check test_stitch - with chunks - with map") { + test("Check test_stitch - no map - no chunks") { config "../../../conf/test_stitch.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" + chunks = null + map = null publish_all = true } } @@ -31,15 +33,13 @@ nextflow_pipeline { } } - test("Check test_stitch - no chunks - no map") { + test("Check test_stitch - with map - with chunks") { config "../../../conf/test_stitch.config" when { params { publish_dir_mode = "copy" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' outdir = "$outputDir" - chunks = null - map = null publish_all = true } } diff --git a/workflows/phaseimpute/tests/test_stitch.nf.test.snap b/workflows/phaseimpute/tests/test_stitch.nf.test.snap index b5538374..80a4e42d 100644 --- a/workflows/phaseimpute/tests/test_stitch.nf.test.snap +++ b/workflows/phaseimpute/tests/test_stitch.nf.test.snap @@ -1,618 +1,5 @@ { - "Check test_stitch - with chunks - with map": { - "content": [ - { - "workflow size": 32, - "versions": { - "BAMCHREXTRACT": { - "samtools": "1.23" - }, - "BCFTOOLS_CONCAT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_LIGATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_PHASE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_PLUGINSPLIT": { - 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"workflow size": 30, + "workflow size": 32, "versions": { "BAMCHREXTRACT": { - "samtools": 1.23 + "samtools": "1.23" }, "BCFTOOLS_CONCAT": { "bcftools": "1.23.1" @@ -840,7 +227,12 @@ "bcftools": "1.23.1" }, "BGZIP_POSFILE_IMPUTE": { - "tabix": 1.21 + "tabix": "1.21" + }, + "CUSTOM_GENETICMAPCONVERT": { + "r-base": "4.5.3", + "r-data.table": "1.17.8", + "r-janitor": "2.2.1" }, "GAWK_IMPUTED": { "gawk": "5.3.1" @@ -863,7 +255,7 @@ "rsync": "3.4.1" }, "TABIX_TABIX": { - "tabix": 1.21 + "tabix": "1.21" }, "Workflow": { "nf-core/phaseimpute": "v1.2.0dev" @@ -892,6 +284,19 @@ "imputation/stitch/samples/NA19401.stitch.vcf.gz.tbi", "imputation/stitch/samples/NA20359.stitch.vcf.gz", "imputation/stitch/samples/NA20359.stitch.vcf.gz.tbi", + "initialisation", + "initialisation/map_convertion", + "initialisation/map_convertion/1000GP_chr21.glimpse.map", + "initialisation/map_convertion/1000GP_chr21.minimac.map", + "initialisation/map_convertion/1000GP_chr21.plink.map", + "initialisation/map_convertion/1000GP_chr21.stitch.map", + "initialisation/map_convertion/1000GP_chr22.glimpse.map", + "initialisation/map_convertion/1000GP_chr22.minimac.map", + "initialisation/map_convertion/1000GP_chr22.plink.map", + "initialisation/map_convertion/1000GP_chr22.stitch.map", + "initialisation/prepare_genome", + "initialisation/prepare_genome/GRCh38.s.fa.gz.fai", + "initialisation/prepare_genome/GRCh38.s.fa.gz.gzi", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/bcftools-stats-subtypes.txt", @@ -948,6 +353,16 @@ "NA12878.stitch.bcftools_stats.txt:md5,24d54d3ffba3fed39f7824abbf9a7d81", "NA19401.stitch.bcftools_stats.txt:md5,360b697eac096a9b0ae2cc1059659418", "NA20359.stitch.bcftools_stats.txt:md5,6d62a564c7fead78240007ac90bc8e3b", + "1000GP_chr21.glimpse.map:md5,eda05f6e81718e00e83085bb0b07e584", + "1000GP_chr21.minimac.map:md5,ab83755a9804d27b1086e48e2da64992", + "1000GP_chr21.plink.map:md5,57966816771960670e5149fa5c3cec60", + "1000GP_chr21.stitch.map:md5,939930334691cc1730c3c322af8c2c32", + "1000GP_chr22.glimpse.map:md5,d541ba3ef55d3cff7ad3273ba4be7c64", + "1000GP_chr22.minimac.map:md5,1e35445b12cf8dfb1273500223a43a70", + "1000GP_chr22.plink.map:md5,b70cfdef56d870e575ab29374cfcecd3", + "1000GP_chr22.stitch.map:md5,24eea1320e0033b04c5f5e6fb7cff690", + "GRCh38.s.fa.gz.fai:md5,4f4e0ff133e7a05cb469e345f766ca8c", + "GRCh38.s.fa.gz.gzi:md5,09046d9646db2cc5c425f231ce4595d7", "bcftools-stats-subtypes.txt:md5,20f016802c19197bd01da87b5bebf585", "bcftools_stats_indel-lengths.txt:md5,45ceadfb316d18af27006953d095dcb0", "bcftools_stats_vqc_Count_Indels.txt:md5,616f14f3cb0c747a410e5e40baaccc32", @@ -964,19 +379,19 @@ "VCF files": [ [ "all_samples.batch0.stitch.vcf.gz", - "5289493ecc73af7ed0c1b999021fce15" + "a95f947cf1827afcb572299fe6981c38" ], [ "NA12878.stitch.vcf.gz", - "3a06d166ebeeb24ed291fdc2f3a42a66" + "80c046997caae0a5bf18dd1c7e000f19" ], [ "NA19401.stitch.vcf.gz", - "9916b80615dad2939b6f97d882f60b83" + "fc07fd7c84654e77271922a6207cea0d" ], [ "NA20359.stitch.vcf.gz", - "cf07a0cc1d678c906d5c9bbe19ff9a03" + "359d324d5dd9f190a393ba2a9f4d1385" ] ], "CSV files": [ @@ -1002,7 +417,7 @@ } } ], - "timestamp": "2026-05-17T14:22:43.169082186", + "timestamp": "2026-05-17T15:52:20.555565947", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From 6ceebf23d5cb13665a69416bde4da34aaf856e1b Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 20 May 2026 21:47:49 +0200 Subject: [PATCH 2/4] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 279c9b75..a163d331 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#276](https://github.com/nf-core/phaseimpute/pull/276) - Migrate all `params.value` usage to entry workflow. Use groovy map to store parameters for each step. Use nextflow 25.10 for `getGenomeAttribute()`. - [#286](https://github.com/nf-core/phaseimpute/pull/286) - Remove unecessary `saveAs` from config thanks to topic migration. - [#291](https://github.com/nf-core/phaseimpute/pull/291) - Update TEMPLATE to nf-core tools version 4.0.2. +- [#292](https://github.com/nf-core/phaseimpute/pull/292) - Reorganise and rename pipeline level tests. ### `Fixed` From fa7e5da85b6801edd5d43fca2c7636fcf3790550 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 20 May 2026 21:52:05 +0200 Subject: [PATCH 3/4] Fix linting --- workflows/phaseimpute/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf index 80338077..b2160d38 100644 --- a/workflows/phaseimpute/main.nf +++ b/workflows/phaseimpute/main.nf @@ -128,7 +128,7 @@ workflow PHASEIMPUTE { .count() ch_map_branched = ch_map - .branch { meta, map_file -> + .branch { _meta, map_file -> non_empty: map_file empty: true } @@ -308,7 +308,7 @@ workflow PHASEIMPUTE { // if (steps.contains("impute") || steps.contains("all")) { - if (params.tools.split(',').any{ it in ["stitch", "quilt"] }) { + if (tools.any{ tool -> tool in ["stitch", "quilt"] }) { // Transform posfile to tabulated format shared by QUILT and STITCH GAWK_POSFILE_IMPUTE( ch_posfile.map{ From 43119af9fa07a7bf50f5e99f9c4bbd4cf3b8018c Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 20 May 2026 22:03:10 +0200 Subject: [PATCH 4/4] Fix name --- workflows/phaseimpute/tests/test_beagle5.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/phaseimpute/tests/test_beagle5.nf.test.snap b/workflows/phaseimpute/tests/test_beagle5.nf.test.snap index ea18ebb9..c6e79fe7 100644 --- a/workflows/phaseimpute/tests/test_beagle5.nf.test.snap +++ b/workflows/phaseimpute/tests/test_beagle5.nf.test.snap @@ -192,7 +192,7 @@ "nextflow": "26.04.0" } }, - "Check test_beagle5 - with map - with chunks ": { + "Check test_beagle5 - with map - with chunks": { "content": [ { "workflow size": 51,