From 667a439ec471258c50812bfae5238d1bfae402ad Mon Sep 17 00:00:00 2001 From: maxulysse Date: Sat, 13 Apr 2024 11:14:32 +0200 Subject: [PATCH 1/2] fix(CI): add spark profile to all spark tests --- tests/test_gatk4spark.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_gatk4spark.yml b/tests/test_gatk4spark.yml index 5a31bfa77f..6462bd130a 100644 --- a/tests/test_gatk4spark.yml +++ b/tests/test_gatk4spark.yml @@ -49,7 +49,7 @@ - path: results/preprocessing/mapped/ should_exist: false - name: Run default pipeline with gatk4spark and skipping all QC steps - command: nextflow run main.nf -profile test_cache,use_gatk_spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results + command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results tags: - gatk4spark - preprocessing @@ -82,7 +82,7 @@ - path: results/reports/samtools should_exist: false - name: Run save_output_as_bam with gatk4 spark - command: nextflow run main.nf -profile test_cache,use_gatk_spark --save_output_as_bam --outdir results + command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --save_output_as_bam --outdir results tags: - gatk4spark - preprocessing From 5659d3dd323fc88b9de0c2df1b226262ece68940 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Sat, 13 Apr 2024 11:17:54 +0200 Subject: [PATCH 2/2] feat(CHANGELOG): update --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e7c676065..45ad5ed438 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -55,6 +55,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe - [#1420](https://github.com/nf-core/sarek/pull/1420) - Make `-a` a default argument for `bcftools` concat - [#1422](https://github.com/nf-core/sarek/pull/1422) - Fix `Cannot serialize context map` warning - [#1462](https://github.com/nf-core/sarek/pull/1462) - Fix ascat input channels +- [#1463](https://github.com/nf-core/sarek/pull/1463) - Add `spark` profile to all gatk4spark tests ### Removed