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Co-Authored-By: Claude Opus 4.6 <[email protected]>
Co-Authored-By: Claude Opus 4.6 <[email protected]>
…2055) <!-- # 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. - [x] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors). --------- Co-authored-by: Copilot <[email protected]>
<!-- # 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 Closes #2086 - [ ] 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).
<!-- # 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 Closes #2024 - [ ] 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).
…2143) <!-- # 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 Related to #2030 - [ ] 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).
Update vcf_annotate_snpeff subworkflow
Co-authored-by: Claude Opus 4.6 <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Closes: #2107
Co-authored-by: Claude Opus 4.6 <[email protected]> Fixes #2151
## Summary - Replace the hand-rolled `imNotification` / `hook_url` / `slackreport.json` mechanism with the [`nf-slack` plugin](https://seqeralabs.github.io/nf-slack/) - Slack notifications are now configured via the `SLACK_WEBHOOK_URL` environment variable and the plugin's `slack {}` config scope in `nextflow.config` - Remove `assets/slackreport.json`, `assets/adaptivecard.json`, the `imNotification()` function, and the `hook_url` parameter ## Migration Users previously using `--hook_url` or the `HOOK_URL` env var should now set `SLACK_WEBHOOK_URL` instead. The nf-slack plugin handles on-start, on-complete, and on-error notifications automatically. ## Test plan - [ ] Run pipeline with `SLACK_WEBHOOK_URL` set and verify Slack notification is received - [ ] Run pipeline without `SLACK_WEBHOOK_URL` and verify no errors (plugin disabled gracefully) - [ ] Verify email notifications still work as before 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 4.6 <[email protected]>
…eCaller (#2146) ## Summary - Closes #1282 - The pipeline now errors immediately when `--no_intervals` is used with `--joint_germline` and `haplotypecaller`, since GenomicsDB cannot operate without intervals - Sentieon tools (haplotyper, dnascope) are not affected as they don't use GenomicsDB - Separated the missing VQSR resources warning from the `no_intervals` check for clarity ## Test plan - [ ] Run with `--tools haplotypecaller --joint_germline --no_intervals` and confirm the pipeline exits with a clear error message - [ ] Run with `--tools sentieon_haplotyper --joint_germline --no_intervals` and confirm it still works (no error) - [ ] Run normal joint germline HaplotypeCaller with intervals to confirm no regression 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 4.6 <[email protected]>
Co-authored-by: Claude Opus 4.6 <[email protected]> Closes #1437
Co-authored-by: FriederikeHanssen <[email protected]> Co-authored-by: Claude Opus 4.6 <[email protected]> Closes: #2118
Fixing strict syntax errors so that I can test with Nextflow 26.04 The main change is removing if statements from config. You should be able to just remove them without generating tons of false warnings, since the strict syntax can validate process selectors against conditional processes as well. I was able to run the `test` profile with these changes on 26.03.0-edge --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]>
<!-- # 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. - [x] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors).
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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).