Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update sentieon modules to 202308.02 #1487

Merged
merged 4 commits into from
Apr 29, 2024
Merged

Update sentieon modules to 202308.02 #1487

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
c189b6a
Updating sentieon modules to 202308.02
asp8200 Apr 26, 2024
5598939
Updating changelog
asp8200 Apr 26, 2024
944033a
Using monespace font for tools names in dependency table
asp8200 Apr 26, 2024
0aff681
More monospace font
asp8200 Apr 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
49 changes: 27 additions & 22 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev
- [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2`
- [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication
- [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02`

### Fixed

Expand All @@ -23,6 +24,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `sentieon` | 202308.01 | 202308.02 |

### Modules / Subworkflows

### Parameters
Expand Down Expand Up @@ -93,16 +98,16 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| bcftools | 1.17 | 1.18 |
| ensemblvep | 110.0 | 111.0 |
| fgbio | 2.0.2 | 2.1.0 |
| gatk | 4.4.0.0 | 4.5.0.0 |
| gatk-spark | 4.4.0.0 | 4.5.0.0 |
| mosdepth | 0.3.3 | 0.3.6 |
| multiqc | 1.17 | 1.18 |
| samtools | 1.17 | 1.19.2 |
| Dependency | Old version | New version |
| ------------ | ----------- | ----------- |
| `bcftools` | 1.17 | 1.18 |
| `ensemblvep` | 110.0 | 111.0 |
| `fgbio` | 2.0.2 | 2.1.0 |
| `gatk` | 4.4.0.0 | 4.5.0.0 |
| `gatk-spark` | 4.4.0.0 | 4.5.0.0 |
| `mosdepth` | 0.3.3 | 0.3.6 |
| `multiqc` | 1.17 | 1.18 |
| `samtools` | 1.17 | 1.19.2 |

### Modules / Subworkflows

Expand All @@ -111,9 +116,9 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe

### Parameter

| Old name | New name |
| -------------------------- | ------------------------ |
| bcftools_annotations_index | bcftools_annotations_tbi |
| Old name | New name |
| ---------------------------- | -------------------------- |
| `bcftools_annotations_index` | `bcftools_annotations_tbi` |

## [3.4.0](https://github.com/nf-core/sarek/releases/tag/3.4.0) - Pårtetjåkko

Expand Down Expand Up @@ -163,8 +168,8 @@ Pårtetjåkko is a mountain in the south of the park.

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| fastqc | 0.11.9 | 0.12.1 |
| multiqc | 1.15 | 1.17 |
| `fastqc` | 0.11.9 | 0.12.1 |
| `multiqc` | 1.15 | 1.17 |

### Modules / Subworkflows

Expand Down Expand Up @@ -197,9 +202,9 @@ Ráhpajávvre is the Lule Sámi spelling of Rapaselet.

### Dependencies

| Dependency | Old version | New version |
| -------------------------------- | ----------- | ----------- |
| Control-FREEC/assesssignificance | 11.6b | 11.6 |
| Dependency | Old version | New version |
| ---------------------------------- | ----------- | ----------- |
| `Control-FREEC/assesssignificance` | 11.6b | 11.6 |

## [3.3.1](https://github.com/nf-core/sarek/releases/tag/3.3.1) - Biellorippjávrre

Expand All @@ -223,9 +228,9 @@ A lake near the Rapaselet delta.

### Dependencies

| Dependency | Old version | New version |
| ------------- | ----------- | ----------- |
| Control-FREEC | 11.6 | 11.6b |
| Dependency | Old version | New version |
| --------------- | ----------- | ----------- |
| `Control-FREEC` | 11.6 | 11.6b |

## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet

Expand Down Expand Up @@ -342,7 +347,7 @@ Vuoinesluobbalah is a lake close to Bierikjávrre.

### Fixed

- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY [#1085](https://github.com/nf-core/sarek/pull/1085)
- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in `GATK4_CREATESEQUENCEDICTIONARY` [#1085](https://github.com/nf-core/sarek/pull/1085)
- [#1089](https://github.com/nf-core/sarek/pull/1089) - Remove duplicated code
- [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName
- [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094)
Expand Down
16 changes: 8 additions & 8 deletions modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -391,42 +391,42 @@
},
"sentieon/applyvarcal": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/bwamem": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/dedup": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/dnamodelapply": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/dnascope": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/gvcftyper": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/haplotyper": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"sentieon/varcal": {
"branch": "master",
"git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
"git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
"installed_by": ["modules"]
},
"snpeff/download": {
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/applyvarcal/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/applyvarcal/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/bwamem/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/bwamem/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/dedup/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/dedup/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/dnamodelapply/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/dnamodelapply/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/dnascope/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/dnascope/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/gvcftyper/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/gvcftyper/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/haplotyper/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/haplotyper/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/varcal/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/sentieon/varcal/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading