Merge pull request #1473 from maxulysse/spark_again

fix(spark): load spark profile after loading the test profiles

Author: kenibrewer

CHANGELOG.md

@@ -35,7 +35,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
 - [#1422](https://github.com/nf-core/sarek/pull/1422) - Refactoring following `TEMPLATE` sync with `tools` `2.13`
 - [#1431](https://github.com/nf-core/sarek/pull/1431) - Using docker.containerOptions instead of docker.runOptions. Clearing containerOptions for SPARK modules for any kind of supported container engine
 - [#1439](https://github.com/nf-core/sarek/pull/1439) - Replacing the local module `BUILD_INTERVALS` with the nf-core module `GAWK`
-- [#1456](https://github.com/nf-core/sarek/pull/1456), [#1472](https://github.com/nf-core/sarek/pull/1472) - Revert usage of docker.runOptions. Add an empty docker.runOptions when using the new `spark` profile
+- [#1456](https://github.com/nf-core/sarek/pull/1456), [#1472](https://github.com/nf-core/sarek/pull/1472), [#1473](https://github.com/nf-core/sarek/pull/1473) - Revert usage of docker.runOptions. Add an empty docker.runOptions when using the new `spark` profile
 - [#1457](https://github.com/nf-core/sarek/pull/1457) - Update all modules
 - [#1466](https://github.com/nf-core/sarek/pull/1466) - Update `VEP`
 
@@ -63,6 +63,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
 - [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `vep_cache_version` params to `validationSchemaIgnoreParams` to fix [#1454](https://github.com/nf-core/sarek/issues/1454)
 - [#1471](https://github.com/nf-core/sarek/pull/1471) - Update `vep_version` params match the actual tool version
 - [#1472](https://github.com/nf-core/sarek/pull/1472) - Cast `snpeff_db` params as a string to fix issues with Seqera Platform, as [#1471](https://github.com/nf-core/sarek/pull/1471) was not working as expected
+- [#1472](https://github.com/nf-core/sarek/pull/1472) - Load `spark` profile last to avoid issues with `test` profiles
 
 ### Removed
 

nextflow.config

@@ -200,9 +200,6 @@ profiles {
     arm {
         docker.runOptions        = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
-    spark {
-        docker.runOptions        = ''
-    }
     singularity {
         apptainer.enabled      = false
         charliecloud.enabled   = false
@@ -289,6 +286,9 @@ profiles {
     test_full_germline_ncbench_agilent {
         includeConfig 'conf/test_full_germline_ncbench_agilent.config'
     }
+    spark {
+        docker.runOptions        = ''
+    }
 
     // Extra test profiles for more complete CI
     alignment_to_fastq         { includeConfig 'conf/test/alignment_to_fastq.config' }