From 4080924e4a028336664a121417726ee1e0c00c32 Mon Sep 17 00:00:00 2001 From: buehlere Date: Thu, 25 Jul 2024 14:21:22 -0400 Subject: [PATCH 1/3] update standard maf need to grab different standard maf output from genotype variants --- subworkflows/msk/traceback/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/msk/traceback/main.nf b/subworkflows/msk/traceback/main.nf index f35e5482..9fbe77c1 100644 --- a/subworkflows/msk/traceback/main.nf +++ b/subworkflows/msk/traceback/main.nf @@ -41,7 +41,7 @@ workflow TRACEBACK { GENOTYPEVARIANTS_ALL.out.maf .transpose() .branch { - genotyped: it[1] =~ /.*ORG-STD_genotyped.maf/ + genotyped: it[1] =~ /.*STANDARD_genotyped.maf/ } .set{split_genotype_imp} From 1f9e674a0b33c793c531d5590e26734ccd25ed60 Mon Sep 17 00:00:00 2001 From: buehlere Date: Fri, 26 Jul 2024 15:52:04 -0400 Subject: [PATCH 2/3] update image and standard maf --- modules/msk/genotypevariants/all/main.nf | 4 ++-- subworkflows/msk/traceback/main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/msk/genotypevariants/all/main.nf b/modules/msk/genotypevariants/all/main.nf index af50c7b0..f31416bf 100644 --- a/modules/msk/genotypevariants/all/main.nf +++ b/modules/msk/genotypevariants/all/main.nf @@ -5,8 +5,8 @@ process GENOTYPEVARIANTS_ALL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'ghcr.io/msk-access/genotype_variants:0.3.8': - 'ghcr.io/msk-access/genotype_variants:0.3.8' }" + 'ghcr.io/msk-access/genotype_variants:0.3.9': + 'ghcr.io/msk-access/genotype_variants:0.3.9' }" input: // [[patient:null, id:'sample'], standard.bam, standard.bam.bai, [], [], [], []] diff --git a/subworkflows/msk/traceback/main.nf b/subworkflows/msk/traceback/main.nf index 9fbe77c1..f35e5482 100644 --- a/subworkflows/msk/traceback/main.nf +++ b/subworkflows/msk/traceback/main.nf @@ -41,7 +41,7 @@ workflow TRACEBACK { GENOTYPEVARIANTS_ALL.out.maf .transpose() .branch { - genotyped: it[1] =~ /.*STANDARD_genotyped.maf/ + genotyped: it[1] =~ /.*ORG-STD_genotyped.maf/ } .set{split_genotype_imp} From 84735d65d1a8df9581b5c264c6fa4d1161ef88b4 Mon Sep 17 00:00:00 2001 From: buehlere Date: Fri, 26 Jul 2024 16:19:51 -0400 Subject: [PATCH 3/3] Update main.nf.test.snap --- modules/msk/genotypevariants/all/tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/msk/genotypevariants/all/tests/main.nf.test.snap b/modules/msk/genotypevariants/all/tests/main.nf.test.snap index eefaa9ab..d221b9c0 100644 --- a/modules/msk/genotypevariants/all/tests/main.nf.test.snap +++ b/modules/msk/genotypevariants/all/tests/main.nf.test.snap @@ -81,7 +81,7 @@ "patient": "c-id" }, [ - "197-ORG-STD_genotyped.maf:md5,8a140bbb7af1c291e8597866fb9d6bb9", + "197-ORG-STD_genotyped.maf:md5,e430edb08476cf771fdb608b646ccfb7", "197-STANDARD_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7" ] ] @@ -96,7 +96,7 @@ "patient": "c-id" }, [ - "197-ORG-STD_genotyped.maf:md5,8a140bbb7af1c291e8597866fb9d6bb9", + "197-ORG-STD_genotyped.maf:md5,e430edb08476cf771fdb608b646ccfb7", "197-STANDARD_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7" ] ] @@ -106,6 +106,6 @@ ] } ], - "timestamp": "2024-06-18T14:18:29.181063" + "timestamp": "2024-07-26T16:18:25.671112" } } \ No newline at end of file