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Merge pull request #577 from maxulysse/dev_release_checklist
update RELEASE_CHECKLIST
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.github/RELEASE_CHECKLIST.md

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1. Check that everything is ready to go
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- Desired [PRs](https://github.com/nf-core/sarek/pulls) are merged
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- [GitHub Actions](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+CI%22) are passing on `dev`
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- [nf-core linting](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+linting%22) are passing on `dev`
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- [GHA CI](https://github.com/nf-core/sarek/actions/workflows/ci.yml) are passing on `dev`
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- [GHA linting](https://github.com/nf-core/sarek/actions/workflows/linting.yml) are passing on `dev`
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2. Increase version number following [semantic versioning](http://semver.org/spec/v2.0.0.html)
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3. Choose an appropriate codename for the release (if major or minor)
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- i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography)
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4. Sync `dev` and checkout a new branch for the release
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5. Bump version:
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- `nf-core bump-version . <VERSION>`
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- edit `.circleci/config.yml`
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- edit `.github/workflows/ci.yml`
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- edit `conf/base.config`
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- edit `conf/test.config`
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- edit `containers/snpeff/Dockerfile`
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- edit `containers/snpeff/environment.yml`
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- edit `containers/vep/Dockerfile`
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- edit `containers/vep/environment.yml`
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- edit `docs/images/sarek_subway.svg`
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- generate a new `docs/images/sarek_subway.png`
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- edit `docs/images/sarek_workflow.svg`
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- generate a new `docs/images/sarek_workflow.png`
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- edit `CHANGELOG`
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13. Checkout the `CHANGELOG.md` from `master`
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- `git checkout upstream/master -- CHANGELOG.md`
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14. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
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15. Checkout `docs/images/sarek_workflow.svg` and `docs/images/sarek_workflow.pnh` from `master`
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15. Checkout figures from `master`
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- `git checkout upstream/master -- docs/images/sarek_subway.svg`
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- `git checkout upstream/master -- docs/images/sarek_subway.png`
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- `git checkout upstream/master -- docs/images/sarek_workflow.svg`
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- `git checkout upstream/master -- docs/images/sarek_workflow.png`
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16. Make a PR to `dev`
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17. Wait for review
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18. Merge said PR
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19. Download all new containers to `/sw/data/uppnex/ToolBox/nf-core` on `rackham`
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20. Download newest `nf-core/sarek` to `/data1/containers` on `munin`
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21. Commit and push. Continue making more awesome :metal:
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22. Have fika :cake:
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19. Commit and push. Continue making more awesome :metal:
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20. Have fika :cake:

CHANGELOG.md

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- [#570](https://github.com/nf-core/sarek/pull/570) - Extract mpileup into its own subworkflow; zip mpileup files
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- [#571](https://github.com/nf-core/sarek/pull/571) - Including and using GATK4's mergeVcfs
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- [#572](https://github.com/nf-core/sarek/pull/572) - Adjusted subway map svg for firefox compatibility
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- [#577](https://github.com/nf-core/sarek/pull/577) - Update `RELEASE_CHECKLIST`
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- [#578](https://github.com/nf-core/sarek/pull/578) - Updated module deeptools/bamcoverage
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- [#585](https://github.com/nf-core/sarek/pull/585) - Remove explicit BAM to CRAM conversion after MarkduplicatesSpark; tool does it internally
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- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`

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