From 02611372e834579548c5a5c74f774b845199c27a Mon Sep 17 00:00:00 2001 From: Daniel Schmitz Date: Thu, 31 Oct 2024 15:54:38 +0100 Subject: [PATCH] Fixed join in test --- .../local/methylation/tests/main.nf.test | 6 +- .../local/methylation/tests/main.nf.test.snap | 262 ++++++++++++++---- 2 files changed, 219 insertions(+), 49 deletions(-) diff --git a/subworkflows/local/methylation/tests/main.nf.test b/subworkflows/local/methylation/tests/main.nf.test index bccd3f08..721ee368 100644 --- a/subworkflows/local/methylation/tests/main.nf.test +++ b/subworkflows/local/methylation/tests/main.nf.test @@ -60,7 +60,11 @@ nextflow_workflow { """ input[0] = SHORT_VARIANT_CALLING.out.snp_calls_vcf input[1] = SHORT_VARIANT_CALLING.out.snp_calls_tbi - input[2] = MINIMAP2_ALIGN.out.bam.join(MINIMAP2_ALIGN.out.index) + input[2] = MINIMAP2_ALIGN.out.bam + .join(MINIMAP2_ALIGN.out.index) + .map { meta, bam, bai -> + [ [ id : meta.id ], bam, bai ] + } input[3] = PREPARE_GENOME.out.fasta input[4] = PREPARE_GENOME.out.fai """ diff --git a/subworkflows/local/methylation/tests/main.nf.test.snap b/subworkflows/local/methylation/tests/main.nf.test.snap index 36c1d8e6..ad7b725d 100644 --- a/subworkflows/local/methylation/tests/main.nf.test.snap +++ b/subworkflows/local/methylation/tests/main.nf.test.snap @@ -3,22 +3,96 @@ "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_2.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_2.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ] ], "2": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ], "bed": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_2.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "tbi": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_2.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ] ], "versions": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ] } ], @@ -26,7 +100,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:46:11.106260205" + "timestamp": "2024-10-31T14:57:25.732089648" }, "1 sample - bed unphased - stub": { "content": [ @@ -37,7 +111,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -46,7 +120,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -59,7 +133,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "tbi": [ @@ -68,7 +142,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -81,7 +155,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:50:57.288737262" + "timestamp": "2024-10-31T15:06:21.337874852" }, "1 sample - [] unphased - stub": { "content": [ @@ -92,7 +166,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -101,7 +175,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -114,7 +188,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "tbi": [ @@ -123,7 +197,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -136,28 +210,50 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:50:31.158673972" + "timestamp": "2024-10-31T15:05:51.048367417" }, "1 sample - [] phased - stub": { "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "1": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ], "bed": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "tbi": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ] } ], @@ -165,7 +261,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:49:30.433111552" + "timestamp": "2024-10-31T15:32:25.389277494" }, "1 sample - [] unphased": { "content": [ @@ -176,7 +272,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -185,7 +281,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + "test_modkit_pileup.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" ] ], "2": [ @@ -198,7 +294,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "tbi": [ @@ -207,7 +303,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + "test_modkit_pileup.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" ] ], "versions": [ @@ -220,28 +316,76 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:47:07.381639824" + "timestamp": "2024-10-31T15:02:10.762856486" }, "1 sample - bed phased": { "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ] ], "2": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ], "bed": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "tbi": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup_1.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ], + [ + { + "id": "test" + }, + "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + ] ], "versions": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ] } ], @@ -249,28 +393,50 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:48:06.699480675" + "timestamp": "2024-10-31T15:03:16.264718303" }, "1 sample - bed phased - stub": { "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "1": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ], "bed": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "tbi": [ - + [ + { + "id": "test" + }, + "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b", + "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711" ] } ], @@ -278,7 +444,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:49:57.199128201" + "timestamp": "2024-10-31T15:32:58.055229101" }, "1 sample - bed unphased": { "content": [ @@ -289,7 +455,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -298,7 +464,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + "test_modkit_pileup.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" ] ], "2": [ @@ -311,7 +477,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_modkit_pileup.bed.gz:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "tbi": [ @@ -320,7 +486,7 @@ "id": "test", "num_intervals": 1 }, - "test.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" + "test_modkit_pileup.bed.gz.tbi:md5,ec06685d85d15d8f118a789a9ccc42ad" ] ], "versions": [ @@ -333,6 +499,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:49:03.326133423" + "timestamp": "2024-10-31T15:04:23.241619315" } } \ No newline at end of file