Merge pull request #1463 from maxulysse/fix_spark_MD

fix(CI): add spark profile to all spark tests

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
 

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