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Update modules #822

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merged 34 commits into from
Nov 14, 2022
Merged

Update modules #822

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9b391b5
update easy modules
FriederikeHanssen Nov 9, 2022
77db1e7
update mappers
FriederikeHanssen Nov 9, 2022
0a09464
update mappers
FriederikeHanssen Nov 9, 2022
c509474
Merge remote-tracking branch 'origin/modules_update' into modules_update
FriederikeHanssen Nov 9, 2022
d73d32e
update markduplicates
FriederikeHanssen Nov 10, 2022
f50d9d4
fix dragmap index
FriederikeHanssen Nov 10, 2022
66ae278
update tiddit
FriederikeHanssen Nov 10, 2022
8c88760
update changelog
FriederikeHanssen Nov 10, 2022
92fc3d4
correct versions
FriederikeHanssen Nov 10, 2022
4014ded
merge upstream/dev
FriederikeHanssen Nov 10, 2022
008ba1f
Update fastp
FriederikeHanssen Nov 10, 2022
2f03e4a
UPdate samtools view
FriederikeHanssen Nov 10, 2022
2fedc52
Update workflows/sarek.nf
FriederikeHanssen Nov 10, 2022
a33a2c2
update samtools/collatefastq
FriederikeHanssen Nov 10, 2022
e1347a9
comment empty input channels
FriederikeHanssen Nov 10, 2022
b27f0df
update deepvariant
FriederikeHanssen Nov 10, 2022
deb4ed4
Update bcftools
FriederikeHanssen Nov 10, 2022
382b1f7
Update freebayes
FriederikeHanssen Nov 11, 2022
7f3e8b0
merge upstream/dev
FriederikeHanssen Nov 11, 2022
e03d837
update CHANGELOG
FriederikeHanssen Nov 11, 2022
e7b76e3
fix channel input
FriederikeHanssen Nov 11, 2022
6f0b61a
remove accidental sambamba addition
FriederikeHanssen Nov 11, 2022
5de1bfb
update dragmap
FriederikeHanssen Nov 11, 2022
1d8065b
uuuuugh more meta2 map issues
FriederikeHanssen Nov 11, 2022
c9967ab
formatting
FriederikeHanssen Nov 11, 2022
4495e34
update samtools
FriederikeHanssen Nov 13, 2022
835c11b
some checksums
FriederikeHanssen Nov 13, 2022
0f8cb71
remove tmb test files
FriederikeHanssen Nov 13, 2022
01843c0
dragen test always using docker
FriederikeHanssen Nov 13, 2022
750bc31
dragmap update causes segementation fault
FriederikeHanssen Nov 13, 2022
bd2884b
new dragmpa version has segmentation dump faults
FriederikeHanssen Nov 13, 2022
9da7e76
dragmap version was never reported
FriederikeHanssen Nov 13, 2022
f7b05dd
md5sums
FriederikeHanssen Nov 14, 2022
edc29d3
update changelog
FriederikeHanssen Nov 14, 2022
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38 changes: 38 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#806](https://github.com/nf-core/sarek/pull/806) - Split up `modules.config` file
- [#810](https://github.com/nf-core/sarek/pull/810) - Update CHANGELOG
- [#821](https://github.com/nf-core/sarek/pull/821) - Change `replace` to `putIfAbsent` for automatic search of `input` if none is provided to avoid overwriting values
- [#822](https://github.com/nf-core/sarek/pull/822) - Update modules with `nf-core modules update -a`: Update GATK version to 4.3.0

### Fixed

Expand All @@ -47,6 +48,43 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------------------- | ----------- | ----------- | ----------------------------- |
| `ascat` | 3.0.0 | unchanged |
| `bcftools` | 1.15.1 | unchanged |
| `bwa-mem2` | 2.2.1 | unchanged |
| `bwa` | 0.7.17 | unchanged |
| `cancerit-allelecount` | 4.3.0 | unchanged |
| `cnvkit` | 0.9.9 | unchanged |
| `control-freec` | 11.6 | unchanged |
| `deepvariant` | 1.3.0 | unchanged |
| `dragmap` | 1.2.1 | unchanged |
| `ensembl-vep` | 106.1 | unchanged | //should we update this here? |
FriederikeHanssen marked this conversation as resolved.
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| `fastp` | 0.23.2 | unchanged |
| `fastqc` | 0.11.9 | unchanged |
| `fgbio` | 2.0.2 | unchanged |
| `freebayes` | 1.3.5 | unchanged |
| `gatk4` | 4.2.6.1 | 4.3.0.0 |
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| `gawk` | 5.1.0 | unchanged |
| `manta` | 1.6.0 | unchanged |
| `mosdepth` | 0.3.3 | unchanged |
| `msisensor-pro` | 1.2.0 | unchanged |
| `multiqc` | 1.13a | unchanged |
| `openjdk` | 8.0.312 | unchanged |
| `p7zip` | 15.09 | unchanged |
| `pigz` | 2.3.4 | unchanged |
| `samblaster` | 0.1.26 | unchanged |
| `samtools` | 1.15.1 | unchanged |
| `sed` | 4.7 | unchanged |
| `snpeff` | 5.1 | unchanged |
| `strelka` | 2.9.10 | unchanged |
| `svdb` | 2.6.1 | unchanged |
| `tabix` | 1.11 | unchanged |
| `tiddit` | 3.1.0 | 3.3.2 |
| `vcftools` | 0.1.16 | unchanged |

## [3.0.2](https://github.com/nf-core/sarek/releases/tag/3.0.2) - Lájtávrre

Lájtávrre is a lake you can see from the Skierfe mountain, formed by the Rapaätno river.
Expand Down
72 changes: 35 additions & 37 deletions modules.json
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Expand Up @@ -20,11 +20,11 @@
},
"bwa/index": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65"
},
"bwa/mem": {
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "277f4d693a00471690b66598d167bbca78bbe232"
},
"bwamem2/index": {
"branch": "master",
Expand Down Expand Up @@ -76,31 +76,31 @@
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0"
},
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},
"dragmap/align": {
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "d6363b7ea1b54715677f971a30d417790ee6a0e6"
},
"dragmap/hashtable": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "d6363b7ea1b54715677f971a30d417790ee6a0e6"
},
"ensemblvep": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
},
"fastp": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
},
"fastqc": {
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "3dd73937b084b547f9272bc901e0f120a7913fd8"
},
"fgbio/callmolecularconsensusreads": {
"branch": "master",
Expand All @@ -120,104 +120,103 @@
},
"gatk4/applybqsr": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/applybqsrspark": {
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/applyvqsr": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/baserecalibrator": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/baserecalibratorspark": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
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},
"gatk4/cnnscorevariants": {
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
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"gatk4/createsequencedictionary": {
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
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},
"gatk4/gatherpileupsummaries": {
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/genomicsdbimport": {
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
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"branch": "master",
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/haplotypecaller": {
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},
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"branch": "master",
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"patch": "modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff"
"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/markduplicatesspark": {
"branch": "master",
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/mergemutectstats": {
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},
"gatk4/mergevcfs": {
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"gatk4/mutect2": {
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},
"gatk4/variantrecalibrator": {
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"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
},
"manta/germline": {
"branch": "master",
Expand Down Expand Up @@ -258,7 +257,7 @@
},
"samtools/collatefastq": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "1f3f03be37ae893e6e68469e29d3461519e274de"
},
"samtools/convert": {
"branch": "master",
Expand Down Expand Up @@ -286,8 +285,7 @@
},
"samtools/view": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"patch": "modules/nf-core/samtools/view/samtools-view.diff"
"git_sha": "202683bfc98ddecdd456ea73268e330bca2e5c5a"
},
"snpeff": {
"branch": "master",
Expand Down Expand Up @@ -315,7 +313,7 @@
},
"tiddit/sv": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "89f98091ac9e1653657b9e324e394b158d723a4f"
},
"untar": {
"branch": "master",
Expand Down
22 changes: 19 additions & 3 deletions modules/nf-core/bwa/index/main.nf
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10 changes: 10 additions & 0 deletions modules/nf-core/bwa/index/meta.yml
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2 changes: 1 addition & 1 deletion modules/nf-core/bwa/mem/main.nf
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5 changes: 5 additions & 0 deletions modules/nf-core/bwa/mem/meta.yml
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