Added pcr-indel-model param for GATK HaplotypeCaller #1841
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<!-- # nf-core/sarek pull request Many thanks for contributing to nf-core/sarek! Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors). --------- Co-authored-by: Friederike Hanssen <[email protected]> Co-authored-by: Friederike Hanssen <[email protected]> Co-authored-by: tdanhorn <[email protected]> Co-authored-by: Thomas <[email protected]>
kjellinjonas
requested review from
FriederikeHanssen and
maxulysse
as code owners
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Hey! I think you might be running of a n old dev branch. BEfore you continue, maybe merge dev into your current branch to cut down on changed files and get all those merge conflicts resolved. |
FriederikeHanssen
requested changes
Mar 24, 2025
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@kjellinjonas can you merge dev again? I have the feeling the failing tests are related to that |
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Introduces a parameter to configure the
pcr-indel-modelin GATK HaplotypeCaller. The default "CONSERVATIVE" setting is not ideal for e.g. PCR-free libraries. Allowing users to change this improves indel calling accuracy for such libraries.PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).