Merge pull request #169 from MaxUlysse/LatestPolish

Last minute changes to include to 2.6

.github/RELEASE_CHECKLIST.md

@@ -0,0 +1,45 @@
+# Release checklist
+
+> This checklist is for our own reference, to help us prepare a new release
+
+1. Check that everything is ready to go
+   - Desired [PRs](https://github.com/nf-core/sarek/pulls) are merged
+   - [GitHub Actions](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+CI%22) are passing on `dev`
+   - [nf-core linting](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+linting%22) are passing on `dev`
+2. Increase version number following [semantic versioning](http://semver.org/spec/v2.0.0.html)
+3. Choose an appropriate codename for the release (if major or minor)
+   - i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography)
+4. Sync `dev` and checkout a new branch for the release
+5. Bump version:
+   - `.nf-core bump-version . 2.6`
+   - edit `.circleci/config.yml`
+   - edit `.github/workflows/ci.yml`
+   - edit `conf/base.config`
+   - edit `conf/test.config`
+   - edit `containers/snpeff/Dockerfile`
+   - edit `containers/snpeff/environment.yml`
+   - edit `containers/vep/Dockerfile`
+   - edit `containers/vep/environment.yml`
+   - edit `docs/images/sarek_workflow.svg`
+   - generate a new `docs/images/sarek_workflow.png`
+   - edit `CHANGELOG`
+6. Make a PR to `master`
+7. Wait for reviews
+8. Merge said PR
+9. Make a [release](https://github.com/nf-core/sarek/releases) on GitHub
+10. Update [bio.tools](https://bio.tools/Sarek) with the new release details
+11. RT the nf-core automated tweet about the new released version
+12. Make a new branch from `dev`
+13. Checkout the `CHANGELOG.md` from `master`
+    - `git checkout upstream/master -- CHANGELOG.md`
+14. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
+15. Checkout `docs/images/sarek_workflow.svg` and `docs/images/sarek_workflow.pnh` from `master`
+    - `git checkout upstream/master -- docs/images/sarek_workflow.svg`
+    - `git checkout upstream/master -- docs/images/sarek_workflow.png`
+16. Make a PR to `dev`
+17. Wait for review
+18. Merge said PR
+19. Download all new containers to `/sw/data/uppnex/ToolBox/nf-core` on `rackham`
+20. Download newest `nf-core/sarek` to `/data1/containers` on `munin`
+21. Commit and push. Continue making more awesome :metal:
+22. Have fika :cake:

.github/workflows/ci.yml

@@ -46,9 +46,7 @@ jobs:
       - name: Pull docker image
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
           docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
-          docker tag nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }} nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
       - name: Run annotation test
         run: nextflow run . -profile test_annotation,docker --tools ${{ matrix.tools }}
 
@@ -66,12 +64,9 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+        run: docker pull nfcore/sarek:dev
       - name: Get test data
-        run: |
-          git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
+        run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
       - name: Run germline test
         run: |
           nextflow run . -profile test,docker --input data/testdata/tiny/normal
@@ -96,9 +91,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+        run: docker pull nfcore/sarek:dev
       - name: Run test for minimal genomes
         run: nextflow run . -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
@@ -119,9 +112,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+        run: docker pull nfcore/sarek:dev
       - name: Run ${{ matrix.profile }} test
         run: nextflow run . -profile ${{ matrix.profile }},docker
 
@@ -142,8 +133,6 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+        run: docker pull nfcore/sarek:dev
       - name: Run ${{ matrix.tool }} test
         run: nextflow run . -profile test_tool,docker --tools ${{ matrix.tool }}

CHANGELOG.md

@@ -17,7 +17,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` version `3.3.0`
 - [#163](https://github.com/nf-core/sarek/pull/163) - Add [MSIsensor](https://github.com/ding-lab/msisensor) in tools and container
 - [#164](https://github.com/nf-core/sarek/pull/164) - Add `--no_gatk_spark` params and tests
-- [#166](https://github.com/nf-core/sarek/issues/166) - Add `--markdup_java_options` documentation
+- [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation
+- [#169](https://github.com/nf-core/sarek/pull/169) - Add `RELEASE_CHECKLIST.md` document
 
 ### Changed
 
@@ -69,6 +70,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#158](https://github.com/nf-core/sarek/pull/158) - Fix typo with `params.snpeff_cache` to decide containers for `snpEff`
 - [#164](https://github.com/nf-core/sarek/pull/164) - Fix issues when running with `Sentieon`
 - [#164](https://github.com/nf-core/sarek/pull/164) - Add more VCFs to annotation
+- [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation to fix [#166](https://github.com/nf-core/sarek/issues/166)
 
 ### Deprecated
 
@@ -108,6 +110,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--snpeffDb` is now removed, use `--snpeff_db` instead
 - [#107](https://github.com/nf-core/sarek/pull/107) - `--vepCacheVersion` is now removed, use `--vep_cache_version` instead
 - [#152](https://github.com/nf-core/sarek/pull/152) - Removed `Jenkinsfile`
+- [#169](https://github.com/nf-core/sarek/pull/169) - Removed omicX from README
 
 ## [2.5.2] - Jåkkåtjkaskajekna
 

README.md

@@ -25,7 +25,7 @@ It comes with docker containers making installation trivial and results highly r
     <img title="Sarek Workflow" src="docs/images/sarek_workflow.png" width=40%>
 </p>
 
-It's listed on the [Elixir - Tools and Data Services Registry](https://bio.tools/Sarek), [Dockstore](https://dockstore.org/workflows/github.com/nf-core/sarek) and [omicX - Bioinformatics tools](https://omictools.com/sarek-tool).
+It's listed on [Elixir - Tools and Data Services Registry](https://bio.tools/Sarek) and [Dockstore](https://dockstore.org/workflows/github.com/nf-core/sarek).
 
 ## Quick Start
 
@@ -126,7 +126,7 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 ## Citation
 
 If you use `nf-core/sarek` for your analysis, please cite the `Sarek` pre-print as follows:
-> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 1; peer review: 1 approved]** *F1000Research* 2020, 9:63 [doi: 10.12688/f1000research.16665.1](https://f1000research.com/articles/9-63/v1).
+> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 1; peer review: 2 approved]** *F1000Research* 2020, 9:63 [doi: 10.12688/f1000research.16665.1](https://f1000research.com/articles/9-63/v1).
 
 You can cite the sarek zenodo record for a specific version using the following [doi: 10.5281/zenodo.3476426](https://zenodo.org/badge/latestdoi/184289291)