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Patch release: 1.1.5 #443

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merged 41 commits into from
Feb 8, 2024
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0df7715
Bump 1.1.4 version into dev
nf-core-bot Jan 25, 2024
35c2482
Correct version
nf-core-bot Jan 25, 2024
ba558e8
Correct version
nf-core-bot Jan 25, 2024
c263ea8
Correct v1.1.5dev
nf-core-bot Jan 25, 2024
53d191a
Merge pull request #436 from genomic-medicine-sweden/bump_release_1.1.4
sofstam Jan 25, 2024
6c752a9
add fastp dedup
maxibor Jan 25, 2024
837a239
Merge branch 'fastp_dedup' into dev
maxibor Jan 25, 2024
2570c0f
update changelog
maxibor Jan 25, 2024
e6fdf57
Update CHANGELOG.md
maxibor Jan 26, 2024
6867467
Update nextflow_schema.json
maxibor Jan 26, 2024
47edb12
Update nextflow_schema.json
maxibor Jan 26, 2024
6192222
Include a pre-built kaiju indexes in tutorial.md
Joon-Klaps Jan 26, 2024
1e1c9aa
update changelog.md
Joon-Klaps Jan 26, 2024
0e1d46e
Merge pull request #440 from nf-core/kaiju-prebuilt-indexes
Joon-Klaps Jan 26, 2024
1fed057
Merge branch 'dev' into dedup
sofstam Jan 26, 2024
ea35f93
Prettier
sofstam Jan 26, 2024
3df734d
Template update for nf-core/tools version 2.12
nf-core-bot Jan 29, 2024
821a933
Merge branch 'dev' into nf-core-template-merge-2.12
sofstam Feb 1, 2024
b1250ac
Fix trailing whitespace
sofstam Feb 1, 2024
0411f75
Amount of left-padding spaces
sofstam Feb 1, 2024
080c094
Left-padding spaces and trailing whitespace
sofstam Feb 1, 2024
7e3f119
Apply suggestions from code review
jfy133 Feb 1, 2024
0792d91
Merge pull request #439 from maxibor/dedup
jfy133 Feb 1, 2024
1365e18
Fix linting
sofstam Feb 1, 2024
dba2be8
Prettier
sofstam Feb 1, 2024
0f04072
Prettier
sofstam Feb 1, 2024
568860a
Update README.md
sofstam Feb 1, 2024
cdc36f1
Update nextflow.config
sofstam Feb 1, 2024
98ddd10
Merge pull request #442 from nf-core/nf-core-template-merge-2.12
sofstam Feb 1, 2024
f277760
Bump centrifuge version to hopefully fix mkfifo errors
jfy133 Feb 3, 2024
6b255de
Update CHANGELOG
jfy133 Feb 3, 2024
ba5c7c1
More Changelog updates
jfy133 Feb 3, 2024
de2a4fa
Apply suggestions from code review
jfy133 Feb 3, 2024
003bad1
Update CHANGELOG.md
jfy133 Feb 5, 2024
f9aee61
Kreport friendly container
jfy133 Feb 5, 2024
1e414ef
Merge pull request #444 from nf-core/centrifuge-update
jfy133 Feb 6, 2024
77c0ccb
Bump version
sofstam Feb 8, 2024
9b5dd37
Update CHANGELOG.md
sofstam Feb 8, 2024
ba126d8
Merge pull request #445 from genomic-medicine-sweden/dev
sofstam Feb 8, 2024
47012cc
Apply suggestions from code review
jfy133 Feb 8, 2024
8018d50
Apply suggestions from code review
jfy133 Feb 8, 2024
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Bump centrifuge version to hopefully fix mkfifo errors
jfy133 committed Feb 3, 2024

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commit f2777604a06b93d0604f9777640ec6823e6badbc
6 changes: 6 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -12,8 +12,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

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

### `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]
4 changes: 2 additions & 2 deletions modules.json
Original file line number Diff line number Diff line change
@@ -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": {
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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12 changes: 11 additions & 1 deletion modules/nf-core/centrifuge/kreport/meta.yml

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81 changes: 81 additions & 0 deletions modules/nf-core/centrifuge/kreport/tests/main.nf.test

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47 changes: 47 additions & 0 deletions modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap

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

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