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update modules #619

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merged 7 commits into from
Oct 1, 2024
Merged

update modules #619

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64bea68
update modules
ramprasadn Sep 30, 2024
0e1f3b2
subworkflow changes
ramprasadn Sep 30, 2024
83cd078
update dv subworkflow
ramprasadn Sep 30, 2024
75be509
update changelog
ramprasadn Sep 30, 2024
ec580d8
remove deepvariant
ramprasadn Sep 30, 2024
5374f8d
add latest dv
ramprasadn Sep 30, 2024
a910e42
update align
ramprasadn Sep 30, 2024
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11 changes: 11 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- Update tools [#619](https://github.com/nf-core/raredisease/pull/619)
- Report only variants above 5% heteroplasmy in the clinical vcf file for mitochondria [#616](https://github.com/nf-core/raredisease/pull/616)

### `Fixed`
Expand All @@ -21,6 +22,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Tool updates

| Tool | Old version | New version |
| -------- | ----------- | ----------- |
| bcftools | 1.18 | 1.20 |
| mosdepth | 0.3.6 | 0.3.8 |
| multiqc | 1.21 | 1.25 |
| picard | 3.1.1 | 3.2.0 |
| samtools | 1.19.2 | 1.21 |
| stranger | 0.8.1 | 0.9.1 |
| tabix | 1.19.1 | 1.20 |

## 2.2.0 - Dogmatix [2024-09-13]

### `Added`
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184 changes: 92 additions & 92 deletions modules.json
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4 changes: 1 addition & 3 deletions modules/nf-core/bcftools/annotate/environment.yml
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21 changes: 17 additions & 4 deletions modules/nf-core/bcftools/annotate/main.nf
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87 changes: 55 additions & 32 deletions modules/nf-core/bcftools/annotate/meta.yml
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8 changes: 3 additions & 5 deletions modules/nf-core/bcftools/annotate/tests/bcf.config
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