From 1def4589b496c421b84c22d97dc6f951cf0afc94 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Oct 2022 11:01:24 +0200 Subject: [PATCH 1/4] Fix gatk4/cnnscorevariants modules --- modules.json | 3 ++- modules/nf-core/modules/gatk4/cnnscorevariants/main.nf | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index b5f9469201..492bc65588 100644 --- a/modules.json +++ b/modules.json @@ -143,7 +143,8 @@ }, "gatk4/cnnscorevariants": { "branch": "master", - "git_sha": "5d72500d601432f5396e9022c3a709854197db1a" + "git_sha": "5d72500d601432f5396e9022c3a709854197db1a", + "patch": "modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff" }, "gatk4/createsequencedictionary": { "branch": "master", diff --git a/modules/nf-core/modules/gatk4/cnnscorevariants/main.nf b/modules/nf-core/modules/gatk4/cnnscorevariants/main.nf index a1bb381134..f251155ce3 100644 --- a/modules/nf-core/modules/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/modules/gatk4/cnnscorevariants/main.nf @@ -6,7 +6,7 @@ process GATK4_CNNSCOREVARIANTS { if (params.enable_conda) { exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers." } - container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package + container "broadinstitute/gatk:4.2.6.1" //Biocontainers is missing a package input: tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals) From 7b2da5836506602afa328187e03039e02b088dd6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Oct 2022 11:03:43 +0200 Subject: [PATCH 2/4] add diff file for gatk4/cnnscorevariants module --- .../cnnscorevariants/gatk4-cnnscorevariants.diff | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff diff --git a/modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff b/modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff new file mode 100644 index 0000000000..3630da2ce2 --- /dev/null +++ b/modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff @@ -0,0 +1,14 @@ +Changes in module 'nf-core/modules/gatk4/cnnscorevariants' +--- modules/nf-core/modules/gatk4/cnnscorevariants/main.nf ++++ modules/nf-core/modules/gatk4/cnnscorevariants/main.nf +@@ -6,7 +6,7 @@ + if (params.enable_conda) { + exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers." + } +- container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package ++ container "broadinstitute/gatk:4.2.6.1" //Biocontainers is missing a package + + input: + tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals) + +************************************************************ From 0178520a6d80703d5f5da7a2154851c24c56f5ee Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Oct 2022 11:03:51 +0200 Subject: [PATCH 3/4] update CHANGELOG --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 22123751fc..482824c7fe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,12 +12,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - [#762](https://github.com/nf-core/sarek/pull/762) - Back to dev -- [#762](https://github.com/nf-core/sarek/pull/762), [#768](https://github.com/nf-core/sarek/pull/768) - Update deepvariant module +- [#762](https://github.com/nf-core/sarek/pull/762) - Update deepvariant module ### Fixed - [#762](https://github.com/nf-core/sarek/pull/762) - Polish CHANGELOG + figures - [#766](https://github.com/nf-core/sarek/pull/766) - Align box description in subway map +- [#768](https://github.com/nf-core/sarek/pull/768) - Use double quotes to fix import of singularity images for deepvariant module +- [#769](https://github.com/nf-core/sarek/pull/769) - Use double quotes to fix import of singularity images for gatk4/cnnscorevariants module ### Deprecated From 76223d60ed5221572e37b29a057f984e17f71a22 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Oct 2022 11:04:29 +0200 Subject: [PATCH 4/4] fix CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 482824c7fe..2437a1a7ef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#762](https://github.com/nf-core/sarek/pull/762) - Polish CHANGELOG + figures - [#766](https://github.com/nf-core/sarek/pull/766) - Align box description in subway map - [#768](https://github.com/nf-core/sarek/pull/768) - Use double quotes to fix import of singularity images for deepvariant module -- [#769](https://github.com/nf-core/sarek/pull/769) - Use double quotes to fix import of singularity images for gatk4/cnnscorevariants module +- [#770](https://github.com/nf-core/sarek/pull/770) - Use double quotes to fix import of singularity images for gatk4/cnnscorevariants module ### Deprecated