From e04f7aa978dfc1f42d2cb4768292a5384d747084 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Thu, 14 Mar 2024 09:20:13 +0000 Subject: [PATCH 1/2] Removing option -stub from nf-cmd in the test of pipeline-download --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 08622fd516..48fe5d0a94 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -69,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results From 7513b7baa3aa114e7a829ae964242f1b85992d3e Mon Sep 17 00:00:00 2001 From: asp8200 Date: Thu, 14 Mar 2024 09:31:10 +0000 Subject: [PATCH 2/2] Updating changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3cab8fd7f..ff9a7da38f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local modules - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local subworkflows - [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11` +- [#1385](https://github.com/nf-core/sarek/pull/1385), [#1436](https://github.com/nf-core/sarek/pull/1436) - Sync `TEMPLATE` with `tools` `2.12` - [#1408](https://github.com/nf-core/sarek/pull/1408), [#1412](https://github.com/nf-core/sarek/pull/1412) - Updating samtools to v1.19.2 - except in GATK/markduplicates. (Temporarily disabled nf-test for bwamem2/mem.) - [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporarily disable sentieon related tests - [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates.