Merge pull request #1039 from maxulysse/concatenate_singularity

Remove concatenate_vcfs tests with singularity

.github/workflows/pytest-workflow.yml

@@ -40,26 +40,28 @@ jobs:
           - "22.10.1"
           - "latest-everything"
         exclude:
-          - profile: "conda"
-            tags: umi
-          - profile: "conda"
-            tags: deepvariant
-          - profile: "conda"
-            tags: haplotypecaller
-          - profile: "conda"
-            tags: merge
-          - profile: "conda"
-            tags: snpeff
-          - profile: "conda"
-            tags: vep
-          - profile: "conda"
+          # - profile: "conda"
+          #   tags: concatenate_vcfs
+          # - profile: "conda"
+          #   tags: deepvariant
+          # - profile: "conda"
+          #   tags: haplotypecaller
+          # - profile: "conda"
+          #   tags: merge
+          # - profile: "conda"
+          #   tags: snpeff
+          # - profile: "conda"
+          #   tags: umi
+          # - profile: "conda"
+          #   tags: validation_checks
+          # - profile: "conda"
+          #   tags: vep
+          - profile: "singularity"
             tags: concatenate_vcfs
           - profile: "singularity"
             tags: merge
           - profile: "singularity"
             tags: validation_checks
-          - profile: "conda"
-            tags: validation_checks
     env:
       NXF_ANSI_LOG: false
       TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"

CHANGELOG.md

@@ -63,6 +63,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#998](https://github.com/nf-core/sarek/pull/998) - Remove parallelization within a sample for `Manta`
 - [#1014](https://github.com/nf-core/sarek/pull/1014) - Fix calls to `ensemblvep` and `snpeff` containers
 - [#1022](https://github.com/nf-core/sarek/pull/1022) - Fix call to variantrecalibrator. (Making sure that dbsnp_vqsr, known_indels_vqsr and known_snps_vqsr are channels, and not strings.)
+- [#1039](https://github.com/nf-core/sarek/pull/1039) - Remove concatenate_vcfs tests with singularity, as they are failing due to not enough space on GHA runners
 
 ### Deprecated