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fix(CI): add spark profile to all spark tests #1463

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merged 3 commits into from
Apr 13, 2024
Merged

fix(CI): add spark profile to all spark tests #1463

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667a439
fix(CI): add spark profile to all spark tests
maxulysse Apr 13, 2024
a2e24f6
Merge branch 'dev' into fix_spark_MD
maxulysse Apr 13, 2024
5659d3d
feat(CHANGELOG): update
maxulysse Apr 13, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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4 changes: 2 additions & 2 deletions tests/test_gatk4spark.yml
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Expand Up @@ -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
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I missed a bunch of discussion around this. What is tl;dr that we have a double spark profile?

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So 1 for the test, and one for the docker.userEmulation that restore proper usage

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ah makes sense, so users should set spark when runnin it now?

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Yes, I think that was the cleanest option I could think of. And if people need, they can use a custom config easily

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makes sense :)

tags:
- gatk4spark
- preprocessing
Expand Down Expand Up @@ -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
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