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Fix: Cloud Storage objects are immutable on GCP #1494

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merged 11 commits into from
May 3, 2024
Merged

Fix: Cloud Storage objects are immutable on GCP #1494

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021ec5f
fix(sort): fix issue with sorting false on gcp
maxulysse May 2, 2024
b7e3523
fix(doi): fix multiple doi print
maxulysse May 2, 2024
adb0ecd
fix(manifest): fix doi in manifest
maxulysse May 2, 2024
c8817f9
code polish
maxulysse May 2, 2024
ce2460b
update CHANGELOG
maxulysse May 2, 2024
9f6903e
Update subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
maxulysse May 2, 2024
7a8a860
let's keep the space and just handle them
maxulysse May 2, 2024
0f682d5
deal with multiple DOI properly
maxulysse May 2, 2024
6a4a189
update CHANGELOG
maxulysse May 2, 2024
c713890
revert changes
maxulysse May 2, 2024
5ab5292
Merge branch 'dev' into sort_gcp
maxulysse May 3, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix
- [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline`
- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491)
- [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest

### Removed
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2 changes: 1 addition & 1 deletion workflows/sarek/main.nf
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Expand Up @@ -879,7 +879,7 @@ workflow SAREK {
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(version_yaml)
ch_multiqc_files = ch_multiqc_files.mix(reports)
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))

MULTIQC (
ch_multiqc_files.collect(),
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