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PR for 2.4.1 release #814

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Merged
TCLamnidis merged 36 commits into from
Nov 30, 2021
Merged

PR for 2.4.1 release #814

TCLamnidis merged 36 commits into from
Nov 30, 2021

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@TCLamnidis TCLamnidis commented Nov 30, 2021

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 and others added 30 commits May 12, 2021 14:22
@jfy133
Merge branch 'nf-core:dev' into dev
e96bbd9
@jfy133
Post release bump
9b3894f
@jfy133
Merge pull request #796 from nf-core/post-release-bump
7b8c73b 
Post release bump
@jfy133
🤦 Add the missing release name of previous release
19b14e0
@TCLamnidis
split bam_trim options by library strandedness
9f82403
@TCLamnidis
Flexible trimming by library strandedness
d50d214
@TCLamnidis
Added new params for bam_trim
eddc97e
@TCLamnidis
Update CHANGELOG.md
47cb415
@TCLamnidis
Cerrected release data of 2.4.0
13523ee
@TCLamnidis
Merge branch 'dev' into trim_by_lib
c6b501c
@TCLamnidis
lint
ef024b5
@TCLamnidis
Sample name as SM in bam read groups. Retain RG info on bam merges
21a9b1f
@TCLamnidis
Update CHANGELOG.md
ef525d1
@TCLamnidis
Flexible filtering of reads for pileupcaller genotyping.
79fedba
@TCLamnidis
Fix typo
0344f01
@TCLamnidis
Correct bam merging output name
6cf64b7
@TCLamnidis
Correct process output for bam merging proceses
5bbcd30
@TCLamnidis
Merge remote-tracking branch 'origin/retain_read_group_info' into pil…
b0232d9 
…eupcaller_params
@TCLamnidis
Update CHANGELOG.md
2db00fb
@TCLamnidis
Merge pull request #810 from nf-core/pileupcaller_params
74e79ba 
Flexible filtering of reads for pileupcaller genotyping.
@jfy133
Update CHANGELOG.md
b5802f9
@TCLamnidis @jfy133
Update CHANGELOG.md
fb124c2 
Co-authored-by: James A. Fellows Yates <[email protected]>
@TCLamnidis
Removed commented old code.
cecbf0b
@jfy133
Merge pull request #807 from nf-core/trim_by_lib
b2e2256 
Trim by lib
@jfy133
Merge branch 'dev' into retain_read_group_info
4228c42
@jfy133
Merge pull request #809 from nf-core/retain_read_group_info
b567e33 
Retain read group info
@jfy133
Merge branch 'nf-core:dev' into dev
325d7eb
@jfy133
Minor QoL updates
53357fa
@jfy133
Merge pull request #812 from jfy133/minor-updates
5b1518b 
Minor updates for 2.4.1
@TCLamnidis
Verision bump 2.4.1
becd256
@jfy133 jfy133 changed the title Dev PR for 2.4.1 release Nov 30, 2021
jfy133
jfy133 approved these changes Nov 30, 2021
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Couple of typos on my part but otherwise looks good 👍

TCLamnidis and others added 2 commits November 30, 2021 09:58
@TCLamnidis @jfy133
Typo
2280fc7 
Co-authored-by: James A. Fellows Yates <[email protected]>
@TCLamnidis @jfy133
Update docs/output.md
95110ce 
Co-authored-by: James A. Fellows Yates <[email protected]>
TCLamnidis
TCLamnidis commented Nov 30, 2021
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jfy133 commented Nov 30, 2021

All tests pass, ignoring nf-core linting because we are still a bit behind 😬

@TCLamnidis TCLamnidis mentioned this pull request Nov 30, 2021
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@TCLamnidis TCLamnidis merged commit 20b0be4 into master Nov 30, 2021
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@apeltzer apeltzer apeltzer approved these changes

@jfy133 jfy133 jfy133 approved these changes

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@TCLamnidis @jfy133 @apeltzer