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update #228

Merged
merged 25 commits into from
Mar 13, 2023
Merged

update #228

merged 25 commits into from
Mar 13, 2023

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yuukiiwa
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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 - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/nanoseq 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 --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).

yuukiiwa and others added 25 commits February 15, 2023 11:24
@yuukiiwa
Merge pull request #216 from nf-core/update_3_1
8e65b61 
Bambu update, bug fixes, and template update
@christopher-hakkaart
Merge pull request #217 from nf-core/update_3_1
adc0832 
remove guppy
@maxulysse
fix custom config for multiqc
2b824f5 
Not sure this actually ever worked.
Thanks to @FranBonath for spotting the issue
@yuukiiwa
Merge pull request #219 from nf-core/maxulysse-patch-1
75cc128 
fix custom config for multiqc
@yuukiiwa
Update CITATIONS.md
d1666b5
@yuukiiwa
Update CITATIONS.md
0820143
@yuukiiwa
Add back demultiplexing
5f4711e
@yuukiiwa
Merge pull request #221 from nf-core/update_3_1
d939006 
Tidy documentation for 3_1
@yuukiiwa
update nanoseq version
e8ad21b
@yuukiiwa
Update CHANGELOG.md
aa0f91f
@yuukiiwa
Update test.config
2fac88e
@yuukiiwa
Update CHANGELOG.md
6bb6694
@yuukiiwa
Update CHANGELOG.md
8bf6db4
Syntax formatting of run_deseq2.r
8f37ff5
@yuukiiwa
Update CHANGELOG.md
a49bd8c
@yuukiiwa
Add files via upload
fb733b3
@yuukiiwa
annotate .collate(12)
0748ea4
@yuukiiwa
Merge pull request #224 from nf-core/DSchreyer-patch-1
7cd4211 
Syntax formatting of run_deseq2.r
@yuukiiwa
Merge pull request #223 from nf-core/update_3_1
2ef8d12 
update CHANGELOG and nextflow.config
@yuukiiwa
address suggestions from Daniel
a1979c4
@yuukiiwa
leaving nf-core subworkflows as it is now
37293dc 
the subworkflow is not updated
@yuukiiwa
Merge pull request #226 from nf-core/update_3_1
5088a4b 
Address Daniel's suggestions
@yuukiiwa
small fix
3be2a78
@yuukiiwa
Merge pull request #227 from nf-core/update_3_1
71fe49f 
small fix
@yuukiiwa
Merge pull request #222 from nf-core/dev
6e563e5 
release 3.1 pull request
@yuukiiwa yuukiiwa merged commit d71927b into update_3_1_dev Mar 13, 2023
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3 participants
@yuukiiwa @christopher-hakkaart @maxulysse