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Release PR for 2.4 #786

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Merged
jfy133 merged 105 commits into from
Sep 14, 2021
Merged

Release PR for 2.4 #786

jfy133 merged 105 commits into from
Sep 14, 2021

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@jfy133
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@jfy133 jfy133 commented Aug 26, 2021 •
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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).

jfy133 added 30 commits April 30, 2021 14:23
@jfy133
Add bcftools stats modules
66d4a68
@jfy133
Add bcftools - still missing output docs
51f5790
@jfy133
Remove unnecessary branching
56a50bc
@jfy133
Add docs and fix compatibility with MVA and VCF2Genomes
f9bc10a
@jfy133
Update output.md
e0fae4e
@jfy133
Remove now uncessary CONTRIBUTING step due to new magic groovy functions
9032bf6
@jfy133
Merge branch 'bcftools' of github.com:nf-core/eager into bcftools
148631d
@jfy133
Software version reporting fixes and additions
3702a07
@jfy133
Update changelog
a47f744
@jfy133
Update CHANGELOG.md
d92bcf2
@jfy133
Merge branch 'major-release-wangen' into bcftools
f2f4ce7
@jfy133
Merge branch 'bcftools' into dev-for-bcftools
5cf6af5
@jfy133
Merge pull request #749 from nf-core/dev-for-bcftools
110d47e 
Get latest dev into bcftools branch
@jfy133
Merge pull request #752 from nf-core/validation-fixes-patch
429e311 
Get upstream fixes for tests to pass
@jfy133
Merge pull request #756 from nf-core/dev
18b49c9 
Get latest dev into wangen base
@jfy133
Add basic functionality for barcode trimming -
a48953e
@jfy133
Add CI tests
5ed9de6
@jfy133
Post release version bump
582dcf5
@jfy133
Markdown linking
831cb5e
@jfy133
Bump pipeline and tool versions
0b5d95a
@jfy133
Merge branch 'dev' into major-release-wangen
8d80552
@jfy133
Merge pull request #764 from nf-core/post-release-update
88fb23b 
Post release version bump
@jfy133
dd additional CI
bdfc5a1
@jfy133
Merge branch 'major-release-wangen' into bcftools
6876e81
@jfy133
Bump vcftools verison to latest
a9f18d3
@jfy133
Fix script
ea7f905
@jfy133
Fix naming conflict when skip AR + running post_ar trim
231ae78
@jfy133
Add AR adapterList removal
342ec92
@jfy133
mardown lint
d95f31c
@jfy133
Input channel in input and not output :grimace:
6807e5c
@jfy133 jfy133 requested a review from a team August 26, 2021 08:18
apeltzer
apeltzer approved these changes Aug 27, 2021
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Bumping versions to 2.4.0 everywhere missing, otherwise looking good 👍🏻

@jfy133 jfy133 requested a review from a team August 27, 2021 13:57
d4straub
d4straub approved these changes Sep 14, 2021
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LGTM, just minor comments.

Linting seems not to work, I guess that is due to the code still being DSL1 instead of DSL2?!

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jfy133 commented Sep 14, 2021 •
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Thanks @d4straub ! Yes, the ancient DSL1 causes linting to fail ;) but I checked manually with the old version

@jfy133 jfy133 merged commit cc66639 into master Sep 14, 2021
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@jfy133 @apeltzer @d4straub