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Fix --three_prime_clip_r{1,2} parameter documentation (fixes #1382) #1383

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merged 6 commits into from
Feb 6, 2024
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Fix --three_prime_clip_r{1,2} parameter documentation (fixes #1382) #1383

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9edbb0a
Fix `--three_prime_clip_r{1,2} parameter` documentation (bug #1382)
tdanhorn Jan 25, 2024
ac0227e
[automated] Fix linting with Prettier
nf-core-bot Jan 25, 2024
f28a615
Merge remote-tracking branch 'nf-core/dev' into HEAD
Feb 6, 2024
d3127e0
Update CHANGELOG.md with #1383
Feb 6, 2024
0c83a2c
Apply suggestions from code review
maxulysse Feb 6, 2024
e5f48b7
Update CHANGELOG.md
maxulysse Feb 6, 2024
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8 changes: 4 additions & 4 deletions .devcontainer/devcontainer.json
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Expand Up @@ -18,11 +18,11 @@
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
"python.linting.pylintPath": "/opt/conda/bin/pylint",
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},

// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
},
},
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}
3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -31,7 +31,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1351](https://github.com/nf-core/sarek/pull/1351) - Fix params name for test profiles (`bcftools_annotations`)
- [#1357](https://github.com/nf-core/sarek/pull/1364) - Fixed bug where samples were dropped while reconstituting BAM files
- [#1373](https://github.com/nf-core/sarek/pull/1373) - Add `chr` prefix to NCBench bed file & enable trimming
- [#1373](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
- [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
- [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation
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### Removed

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4 changes: 2 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -158,15 +158,15 @@
"default": 0,
"fa_icon": "fas fa-cut",
"description": "Remove bp from the 3' end of read 1",
"help_text": "This may remove some unwanted bias from the 3'. Corresponds to the FastP flag `--three_prime_clip_r1`.",
"help_text": "This may remove some unwanted bias from the 3'. Corresponds to the FastP flag `--trim_tail1`.",
"hidden": true
},
"three_prime_clip_r2": {
"type": "integer",
"default": 0,
"fa_icon": "fas fa-cut",
"description": "Remove bp from the 3' end of read 2",
"help_text": "This may remove some unwanted bias from the 3' end. Corresponds to the FastP flag `--three_prime_clip_r2`.",
"help_text": "This may remove some unwanted bias from the 3' end. Corresponds to the FastP flag `--trim_tail2`.",
"hidden": true
},
"trim_nextseq": {
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