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Centrifuge update to address mkfifo clashes #444

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Feb 6, 2024
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9 changes: 8 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- [#439](https://github.com/nf-core/taxprofiler/pull/439) Read deduplication with fastp (added by @maxibor)
- [#440](https://github.com/nf-core/taxprofiler/pull/440) Include pre-built kaiju databases in tutorial.md (added by @Joon-Klaps)
- [#440](https://github.com/nf-core/taxprofiler/pull/440) Include mention of pre-built kaiju databases in tutorial.md (added by @Joon-Klaps)
- [#424](https://github.com/nf-core/taxprofiler/pull/424) Updated to nf-core pipeline template v2.12 (added by @sofstam)

### `Fixed`

- [#444](https://github.com/nf-core/taxprofiler/pull/440) Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133)
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### `Dependencies`

| Tool | Previous version | New version |
| ---------- | ---------------- | ----------- |
| Centrifuge | 1.0.4_beta | 1.0.4.1 |

### `Deprecated`

## v1.1.4 - Augmented Akita Patch [2024-01-24]
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4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -42,12 +42,12 @@
},
"centrifuge/centrifuge": {
"branch": "master",
"git_sha": "7b0b4276fbad744a69c35d3cbf9d55fdfc9491bd",
"git_sha": "32a99bba21c961f8642ddd38fcd4ea2844c10990",
"installed_by": ["modules"]
},
"centrifuge/kreport": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "32a99bba21c961f8642ddd38fcd4ea2844c10990",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
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7 changes: 7 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/environment.yml

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39 changes: 36 additions & 3 deletions modules/nf-core/centrifuge/centrifuge/main.nf

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4 changes: 4 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/meta.yml

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106 changes: 106 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/tests/main.nf.test

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125 changes: 125 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap

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2 changes: 2 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/tests/tags.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/centrifuge/kreport/environment.yml

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22 changes: 17 additions & 5 deletions modules/nf-core/centrifuge/kreport/main.nf

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