diff --git a/CHANGELOG.md b/CHANGELOG.md index eb339d005..7d1434d99 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/nextflow.config b/nextflow.config index 189f7cf68..a5526b67c 100644 --- a/nextflow.config +++ b/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' }