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Annotation code polish #626

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Merged
maxulysse merged 2 commits into from
Jul 8, 2022
Merged

Annotation code polish #626

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9b619fe
remove WARN message about no process matching config selector
maxulysse Jul 8, 2022
e0585de
update CHANGELOG [skip CI]
maxulysse Jul 8, 2022
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -108,7 +108,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is back
- [#590](https://github.com/nf-core/sarek/pull/590) - Fix empty folders during scatter/gather
- [#592](https://github.com/nf-core/sarek/pull/592) - Fix optional resources for Mutect2, GetPileupSummaries, and HaplotypeCaller: issue [#299](https://github.com/nf-core/sarek/issues/299), [#359](https://github.com/nf-core/sarek/issues/359), [#367](https://github.com/nf-core/sarek/issues/367)
- [#598](https://github.com/nf-core/sarek/pull/598), [#614](https://github.com/nf-core/sarek/pull/614) - Remove WARNING message for config selector not matching
- [#598](https://github.com/nf-core/sarek/pull/598), [#614](https://github.com/nf-core/sarek/pull/614), [#626](https://github.com/nf-core/sarek/pull/626) - Remove WARNING message for config selector not matching
- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for correct data type for `params.step`
- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for no empty `--tools` with `--step variant_calling` or `--step annotation`
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
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2 changes: 2 additions & 0 deletions conf/modules.config
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Expand Up @@ -1191,7 +1191,9 @@ process{
pattern: "*{gz,gz.tbi}"
]
}
}

if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge'))) {
withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_SNPEFF:TABIX_BGZIPTABIX' {
publishDir = [
mode: params.publish_dir_mode,
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