8000 Update all modules by maxulysse · Pull Request #1871 · nf-core/sarek · GitHub
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Update all modules #1871

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Update all modules #1871

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b6542a6
nf-core modules update -f -a
maxulysse Apr 17, 2025
249efd1
Merge branch 'dev' into modules_update_all
maxulysse Apr 29, 2025
c606e76
do not copy the tests
maxulysse Apr 29, 2025
38e8ddb
Merge branch 'dev' into modules_update_all
maxulysse May 5, 2025
3271777
update modules
maxulysse May 5, 2025
c041470
fix usage and update default tests
maxulysse May 5, 2025
52a4a50
update snapshots
maxulysse May 5, 2025
2532e55
update CHANGELOG
maxulysse May 5, 2025
ae48a54
update CHANGELOG
maxulysse May 5, 2025
a355e79
update mosdepth and gatk4 in snapshots
maxulysse May 5, 2025
5d8c170
update versions
maxulysse May 5, 2025
31ee4c6
polish
maxulysse May 5, 2025
6e4a4cd
bwamem2mem
maxulysse May 5, 2025
01aafd2
update modules
maxulysse May 7, 2025
7aa8522
update gatk4/intervallisttobed
maxulysse May 7, 2025
d611ccc
update samtools in Markduplicates
maxulysse May 7, 2025
5381737
update CHANGELOG
maxulysse May 7, 2025
cae04eb
update snapshots
maxulysse May 7, 2025
f5584b3
update CHANGELOG
maxulysse May 8, 2025
6ff0632
update modules
maxulysse May 8, 2025
112bf8b
update snapshots
maxulysse May 8, 2025
4bfb1db
update snapshots
maxulysse May 8, 2025
691f363
update snapshot
maxulysse May 8, 2025
309b225
update snapshots
maxulysse May 8, 2025
8a45b18
update snapshots
maxulysse May 8, 2025
403dd9d
update snapshots
maxulysse May 8, 2025
8c3e597
update snapshots
maxulysse May 8, 2025
aa7093d
update freebayes snapshot
maxulysse May 8, 2025
b72d47e
update mpileup snapshots
maxulysse May 8, 2025
9d509e2
update final snapshots
maxulysse May 9, 2025
414e55d
modules update all
maxulysse May 9, 2025
c3de166
update snapshot
maxulysse May 9, 2025
b7c69da
Apply suggestions from code review
SPPearce May 9, 2025
729c963
Merge branch 'dev' into modules_update_all
maxulysse May 13, 2025
9e7f095
update bcftools
maxulysse May 14, 2025
9becb4e
update snapshot
maxulysse May 14, 2025
506cefb
fix stderr tests
maxulysse May 14, 2025
3f5b2c6
same snapshot for same files in all tests
maxulysse May 14, 2025
493301a
Update CHANGELOG.md
maxulysse May 14, 2025
ca6524d
Update CHANGELOG.md
maxulysse May 14, 2025
38fcafd
somehow [ is not registering the same on my computer and GHA
maxulysse May 19, 2025
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20 changes: 16 additions & 4 deletions CHANGELOG.md
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Expand Up @@ -34,10 +34,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `MultiQC` | 1.25.1 | 1.27 |
| `MuSE` | | 2.1.2 |
| Dependency | Old version | New version |
| -------------------------------------- | ----------- | ----------- |
| `bcftools` | 1.20 | 1.21 |
| `ensemblvep` | 113.0 | 113.4 |
| `fastp` | 0.23.4 | 0.24.0 |
| `fgbio` | 2.2.1 | 2.4.0 |
| `gatk4` | 4.5.0.0 | 4.6.1.0 |
| `mosdepth` | 0.3.8 | 0.3.10 |
| `MuSE` | | 2.1.2 |
| `MultiQC` | 1.25.1 | 1.28 |
| `samtools` (in `BWAMEM1_MEM`) | 1.2 | 1.21 |
| `samtools` (in `BWAMEM2_MEM`) | 1.19.2 | 1.21 |
| `samtools` (in `GATK4_MARKDUPLICATES`) | 1.19.2 | 1.21 |
| `sentieon` | 202308.03 | 202503 |
| `tabix` | 1.2 | 1.21 |

### Parameters

Expand Down Expand Up @@ -79,6 +90,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1866](https://github.com/nf-core/sarek/pull/1866) - Migrate pipeline pytest deepvariant tests to nf-test
- [1867](https://github.com/nf-core/sarek/pull/1867) - Migrate pipeline pytest gatk4spark tests to nf-test
- [1868](https://github.com/nf-core/sarek/pull/1868) - Migrate pipeline pytest intervals tests to nf-test
- [1871](https://github.com/nf-core/sarek/pull/1871) - Update all modules
- [1874](https://github.com/nf-core/sarek/pull/1874) - Migrate pipeline pytest joint_calling haplotypecaller tests to nf-test
- [1874](https://github.com/nf-core/sarek/pull/1874) - Migrate pipeline pytest joint_calling mutect2 tests to nf-test
- [1874](https://github.com/nf-core/sarek/pull/1874) - Migrate pipeline pytest mutect2 tests to nf-test
Expand Down
3 changes: 3 additions & 0 deletions conf/test.config
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Expand Up @@ -15,6 +15,9 @@ process {
memory: '15.GB',
time: '1.h'
]
withName:BWAMEM2_INDEX {
memory = { 6.GB }
}
}

params {
Expand Down
213 changes: 105 additions & 108 deletions modules.json
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11 changes: 9 additions & 2 deletions modules/nf-core/ascat/environment.yml
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117 changes: 59 additions & 58 deletions modules/nf-core/ascat/main.nf
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17 changes: 7 additions & 10 deletions modules/nf-core/bcftools/annotate/bcftools-annotate.diff
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4 changes: 3 additions & 1 deletion modules/nf-core/bcftools/annotate/environment.yml
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13 changes: 8 additions & 5 deletions modules/nf-core/bcftools/annotate/main.nf
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3 changes: 3 additions & 0 deletions modules/nf-core/bcftools/annotate/meta.yml
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4 changes: 0 additions & 4 deletions modules/nf-core/bcftools/annotate/tests/bcf.config
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