From 9b9d7d0bd27fc391fdf2b1a27ab7d39e7ea4513d Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Thu, 23 Jan 2025 15:45:50 +0100 Subject: [PATCH] Bump TRGT to 1.5.0 (#7346) --- modules/nf-core/trgt/genotype/environment.yml | 2 +- modules/nf-core/trgt/genotype/main.nf | 4 +- .../trgt/genotype/tests/main.nf.test.snap | 64 +++++++++---------- modules/nf-core/trgt/merge/environment.yml | 2 +- modules/nf-core/trgt/merge/main.nf | 4 +- .../trgt/merge/tests/main.nf.test.snap | 34 +++++----- modules/nf-core/trgt/plot/environment.yml | 2 +- modules/nf-core/trgt/plot/main.nf | 4 +- .../nf-core/trgt/plot/tests/main.nf.test.snap | 16 ++--- 9 files changed, 66 insertions(+), 66 deletions(-) diff --git a/modules/nf-core/trgt/genotype/environment.yml b/modules/nf-core/trgt/genotype/environment.yml index 721e0df3d5f..53b88a1fbd6 100644 --- a/modules/nf-core/trgt/genotype/environment.yml +++ b/modules/nf-core/trgt/genotype/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::trgt=1.2.0" + - "bioconda::trgt=1.5.0" diff --git a/modules/nf-core/trgt/genotype/main.nf b/modules/nf-core/trgt/genotype/main.nf index 3fa0b7b4e59..c4500bd2ae6 100644 --- a/modules/nf-core/trgt/genotype/main.nf +++ b/modules/nf-core/trgt/genotype/main.nf @@ -4,8 +4,8 @@ process TRGT_GENOTYPE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0': - 'biocontainers/trgt:1.2.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/trgt:1.5.0--h9ee0642_0': + 'biocontainers/trgt:1.5.0--h9ee0642_0' }" input: tuple val(meta) , path(bam), path(bai), val(karyotype) diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test.snap b/modules/nf-core/trgt/genotype/tests/main.nf.test.snap index 9e50fb81eb3..ae7bbfd92b8 100644 --- a/modules/nf-core/trgt/genotype/tests/main.nf.test.snap +++ b/modules/nf-core/trgt/genotype/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e" + "test.vcf.gz:md5,e60da9fd3a401595263df8822c3e5044" ] ], "1": [ @@ -15,18 +15,18 @@ { "id": "test" }, - "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37" + "test.spanning.bam:md5,83cc54729b657edbc30670926c357a5f" ] ], "2": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ], "bam": [ [ { "id": "test" }, - "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37" + "test.spanning.bam:md5,83cc54729b657edbc30670926c357a5f" ] ], "vcf": [ @@ -34,19 +34,19 @@ { "id": "test" }, - "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e" + "test.vcf.gz:md5,e60da9fd3a401595263df8822c3e5044" ] ], "versions": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T16:07:55.029938504" + "timestamp": "2025-01-22T16:47:21.469366302" }, "homo sapiens - [bam,bai,[]], [fa,fai], bed - stub": { "content": [ @@ -56,7 +56,7 @@ { "id": "test" }, - "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f" + "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855" ] ], "1": [ @@ -64,18 +64,18 @@ { "id": "test" }, - "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7" + "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6" ] ], "2": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ], "bam": [ [ { "id": "test" }, - "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7" + "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6" ] ], "vcf": [ @@ -83,19 +83,19 @@ { "id": "test" }, - "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f" + "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855" ] ], "versions": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T16:08:33.937952067" + "timestamp": "2025-01-22T16:48:00.564096612" }, "homo sapiens - [bam,bai,XX], [fa,fai], bed - stub": { "content": [ @@ -117,7 +117,7 @@ ] ], "2": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ], "bam": [ [ @@ -136,15 +136,15 @@ ] ], "versions": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T16:16:39.197756426" + "timestamp": "2025-01-22T16:47:47.478426582" }, "homo sapiens - [bam,bai,[]], [fa,fai], bed": { "content": [ @@ -154,7 +154,7 @@ { "id": "test" }, - "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f" + "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855" ] ], "1": [ @@ -162,18 +162,18 @@ { "id": "test" }, - "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7" + "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6" ] ], "2": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ], "bam": [ [ { "id": "test" }, - "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7" + "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6" ] ], "vcf": [ @@ -181,18 +181,18 @@ { "id": "test" }, - "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f" + "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855" ] ], "versions": [ - "versions.yml:md5,b773615cf974b094032306822d32017b" + "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T16:08:07.631383773" + "timestamp": "2025-01-22T16:47:35.097638611" } } \ No newline at end of file diff --git a/modules/nf-core/trgt/merge/environment.yml b/modules/nf-core/trgt/merge/environment.yml index 614dc872b7b..1f49dba6b3a 100644 --- a/modules/nf-core/trgt/merge/environment.yml +++ b/modules/nf-core/trgt/merge/environment.yml @@ -3,4 +3,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::trgt=1.2.0" + - "bioconda::trgt=1.5.0" diff --git a/modules/nf-core/trgt/merge/main.nf b/modules/nf-core/trgt/merge/main.nf index 73e51b02c20..639441f92b2 100644 --- a/modules/nf-core/trgt/merge/main.nf +++ b/modules/nf-core/trgt/merge/main.nf @@ -4,8 +4,8 @@ process TRGT_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0': - 'biocontainers/trgt:1.2.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/trgt:1.5.0--h9ee0642_0': + 'biocontainers/trgt:1.5.0--h9ee0642_0' }" input: tuple val(meta) , path(vcfs), path(tbis) diff --git a/modules/nf-core/trgt/merge/tests/main.nf.test.snap b/modules/nf-core/trgt/merge/tests/main.nf.test.snap index 73f306b0ebf..f8638c2ae60 100644 --- a/modules/nf-core/trgt/merge/tests/main.nf.test.snap +++ b/modules/nf-core/trgt/merge/tests/main.nf.test.snap @@ -5,14 +5,14 @@ "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=1, phased=false, phasedAutodetect=false]", 2, [ - "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067" + "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T14:52:26.329527707" + "timestamp": "2025-01-22T16:48:39.055002317" }, "homo sapiens - 2 VCFs": { "content": [ @@ -20,14 +20,14 @@ "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=1, phased=false, phasedAutodetect=false]", 2, [ - "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067" + "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T14:39:54.475134386" + "timestamp": "2025-01-22T16:48:22.59942164" }, "homo sapiens - 2 VCFs - stub": { "content": [ @@ -41,7 +41,7 @@ ] ], "1": [ - "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067" + "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef" ], "vcf": [ [ @@ -52,15 +52,15 @@ ] ], "versions": [ - "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067" + "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T15:06:23.198648143" + "timestamp": "2025-01-22T16:49:31.819625734" }, "homo sapiens - 1 VCF - --force-single": { "content": [ @@ -68,13 +68,13 @@ "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]", 1, [ - "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067" + "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-15T15:01:59.765895584" + "timestamp": "2025-01-22T16:49:13.2045895" } } \ No newline at end of file diff --git a/modules/nf-core/trgt/plot/environment.yml b/modules/nf-core/trgt/plot/environment.yml index 614dc872b7b..1f49dba6b3a 100644 --- a/modules/nf-core/trgt/plot/environment.yml +++ b/modules/nf-core/trgt/plot/environment.yml @@ -3,4 +3,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::trgt=1.2.0" + - "bioconda::trgt=1.5.0" diff --git a/modules/nf-core/trgt/plot/main.nf b/modules/nf-core/trgt/plot/main.nf index f60fd8a150c..70a06c180e0 100644 --- a/modules/nf-core/trgt/plot/main.nf +++ b/modules/nf-core/trgt/plot/main.nf @@ -4,8 +4,8 @@ process TRGT_PLOT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0': - 'biocontainers/trgt:1.2.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/trgt:1.5.0--h9ee0642_0': + 'biocontainers/trgt:1.5.0--h9ee0642_0' }" input: tuple val(meta) , path(bam), path(bai), path(vcf), path(tbi), val(repeat_id) diff --git a/modules/nf-core/trgt/plot/tests/main.nf.test.snap b/modules/nf-core/trgt/plot/tests/main.nf.test.snap index e8614fde091..c0a0d3535aa 100644 --- a/modules/nf-core/trgt/plot/tests/main.nf.test.snap +++ b/modules/nf-core/trgt/plot/tests/main.nf.test.snap @@ -3,26 +3,26 @@ "content": [ "test.png", [ - "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c" + "versions.yml:md5,280ac168a069db522950dce55feddbae" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-18T13:58:28.083155724" + "timestamp": "2025-01-22T16:50:04.133470512" }, "homo sapiens - [bam, bai, vcf, TEST], fasta, fai, bed": { "content": [ "test_TEST.png", [ - "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c" + "versions.yml:md5,280ac168a069db522950dce55feddbae" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-11-18T13:57:59.291774232" + "timestamp": "2025-01-22T16:49:48.231158363" } } \ No newline at end of file