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CHORE: update all modules #968

Merged
merged 18 commits into from
Apr 27, 2023
Merged

CHORE: update all modules #968

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3538373
update all modules
maxulysse Mar 17, 2023
5f12a65
Merge branch 'dev' into gatk_update
maxulysse Apr 11, 2023
9d18ba2
updating modules
maxulysse Apr 14, 2023
4b93590
add INDEX creation
maxulysse Apr 25, 2023
ed33deb
fix channels
maxulysse Apr 25, 2023
26aa534
typo
maxulysse Apr 25, 2023
a1f46dd
one liner
maxulysse Apr 25, 2023
80ba818
mode modules update
maxulysse Apr 25, 2023
373f6ae
update CHANGELOG
maxulysse Apr 25, 2023
0483672
patch dragmap/hashtable
maxulysse Apr 25, 2023
f4b1620
add ASCAT to updated tools
maxulysse Apr 25, 2023
3d363e5
remove conda tests as they almost always fail
maxulysse Apr 25, 2023
2864be5
remove md5sum
maxulysse Apr 26, 2023
4ee7618
update subworkflow
maxulysse Apr 26, 2023
76eb094
update unzip module
maxulysse Apr 26, 2023
c6303c7
update bcftools
maxulysse Apr 26, 2023
4d377e7
update bcftools related md5sum
maxulysse Apr 27, 2023
7a75269
update paths for untar tests
maxulysse Apr 27, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#936](https://github.com/nf-core/sarek/pull/936) - Add params `donwload_cache` to download annotation cache
- [#942](https://github.com/nf-core/sarek/pull/942) - Update `README.md`
- [#967](https://github.com/nf-core/sarek/pull/967) - Update and detail extensively how to use annotation cache
- [#968](https://github.com/nf-core/sarek/pull/968) - Update all modules

### Fixed

Expand Down Expand Up @@ -64,6 +65,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| `bcftools` | 1.15.1 | 1.16 |
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| `ensembl-vep` | 106.1 | 108.2 |
| `multiqc` | 1.13a | 1.14 |
| `samtools` | 1.16 | 1.17 |
| `svdb` | 2.6.1 | 2.8.1 |

### Modules / Subworkflows
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144 changes: 71 additions & 73 deletions modules.json
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23 changes: 18 additions & 5 deletions modules/nf-core/bcftools/sort/main.nf
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4 changes: 2 additions & 2 deletions modules/nf-core/cat/cat/meta.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/antitarget/main.nf
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4 changes: 3 additions & 1 deletion modules/nf-core/cnvkit/antitarget/meta.yml
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2 changes: 2 additions & 0 deletions modules/nf-core/cnvkit/batch/main.nf
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1 change: 1 addition & 0 deletions modules/nf-core/cnvkit/batch/meta.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/reference/main.nf
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4 changes: 3 additions & 1 deletion modules/nf-core/cnvkit/reference/meta.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/controlfreec/freec/meta.yml
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6 changes: 3 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf
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Empty file modified modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
100755 → 100644
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1 change: 1 addition & 0 deletions modules/nf-core/deepvariant/main.nf
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6 changes: 5 additions & 1 deletion modules/nf-core/deepvariant/meta.yml
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19 changes: 0 additions & 19 deletions modules/nf-core/dragmap/align/dragmap-align.diff
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2 changes: 1 addition & 1 deletion modules/nf-core/dragmap/align/meta.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/dragmap/hashtable/meta.yml
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15 changes: 7 additions & 8 deletions modules/nf-core/ensemblvep/vep/main.nf
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22 changes: 18 additions & 4 deletions modules/nf-core/ensemblvep/vep/meta.yml
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1 change: 0 additions & 1 deletion modules/nf-core/fastp/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/fastp/meta.yml
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5 changes: 3 additions & 2 deletions modules/nf-core/fgbio/callmolecularconsensusreads/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/fgbio/fastqtobam/meta.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/fgbio/groupreadsbyumi/meta.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/freebayes/meta.yml
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