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v1.2 - Bouncy Basenji Release PR #525

Merged
merged 200 commits into from
Oct 3, 2024
Merged

v1.2 - Bouncy Basenji Release PR #525

merged 200 commits into from
Oct 3, 2024

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jfy133
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@jfy133 jfy133 commented Sep 11, 2024

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/taxprofiler 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

jfy133 and others added 30 commits November 9, 2023 19:57
@jfy133
Install module
a58388c
@jfy133
Merge pull request #416 from nf-core/dev
b25350c 
Sync with dev
@jfy133
Add get it working, add to tests, update docs/images/citations
69e0d09
@jfy133
Fix groovy semantic errors
2c24711
@jfy133
update gitignore to ignore nf-test
1a37251
@jfy133
Revert "update gitignore to ignore nf-test"
240634c 
This reverts commit 1a37251.
@jfy133
Fix nonpareil args across all tests
5e853b0
@jfy133
Add nonpareil
a050658
@jfy133
Minor linting
ff16394
@jfy133
Fix channel emission
46bf2b2
@jfy133
Fix module linting
c69b00e
@jfy133
Add nonpareil to valid MultiQC entries
a0d5821
@jfy133
Final linting
c1d12d9
@nf-core-bot
[automated] Fix linting with Prettier
88b8e1a
@jfy133 @LilyAnderssonLee
Apply suggestions from code review
40d1bfa 
Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
@jfy133
Merge pull request #417 from nf-core/add-nonpareil
ffff2e6 
Add nonpareil
@jfy133
Merge branch 'dev' into bouncy-basenji
5ea76e8
@sofstam
Merge dev into bouncy-basenji
f4dd39b
@jfy133
Fix prettier
f00bd54
@jfy133
Remove merge marker
45dd3c9
@jfy133
Merge branch 'bouncy-basenji' into fix-merge-conflict
d9de044
@jfy133
Merge pull request #448 from nf-core/fix-merge-conflict
aa6d088 
Dev to bouncy-basenji
@LilyAnderssonLee
Merge dev into bouncy-basenji
c22f6e9
@LilyAnderssonLee
Merge pull request #455 from LilyAnderssonLee/bouncy-basenji
faf93e9 
Merge dev into bouncy-basenji
@LilyAnderssonLee
update the nanopore and fasta input channel
9373a96
@LilyAnderssonLee
Merge branch 'nf-core:master' into fix-validation
b0d2ad3
@LilyAnderssonLee
add fallback to download pipeline workflow
ff977f6
@LilyAnderssonLee
update nf-validation
b89aba6
@LilyAnderssonLee @jfy133
Update workflows/taxprofiler.nf
d0a58e2 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee
Update taxprofiler.nf
dabc253
@jfy133 jfy133 requested a review from atrull314 September 26, 2024 07:41
@jfy133
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jfy133 commented Sep 26, 2024

@atrull314 could you gvive us the ✔️ ?

jfy133 and others added 21 commits September 26, 2024 10:03
@jfy133 @LilyAnderssonLee
Update docs/output.md
963302f 
Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
@LilyAnderssonLee
clean unsupported small files in tower
e4a4776
@sofstam
Add db_type column to documentation
f7222f6
@sofstam @jfy133
Update docs/usage/tutorials.md
2b8acee 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam @jfy133
Update docs/usage/tutorials.md
d2f109a 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam
Prettier
c5a92e1
@sofstam
Review suggestions
719ac9e
@sofstam
Prettier
7719f2a
@LilyAnderssonLee
Merge pull request #534 from nf-core/tower_yml
7d7d0c7 
Check if all small files are included in tower.yml
@sofstam
James suggestions
270c159
@sofstam @jfy133
Update docs/usage.md
c974db6 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam
Add example of empty db_type
9402b5a
@sofstam
Merge branch 'documentation_release' of https://github.com/sofstam/ta…
1f6775c 
…xprofiler into documentation_release
@sofstam
Prettier
9b64847
@sofstam @jfy133
Update docs/usage.md
d00104a 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam
Review suggestions
80cdb0c
@LilyAnderssonLee
fix missing of filtlong in multiqc report
9d2c86c
@LilyAnderssonLee
Update the changelog
0e2d777
@LilyAnderssonLee
Update CHANGELOG.md
60dc5a0
@LilyAnderssonLee
Merge pull request #536 from nf-core/final_review
7e4734a 
Overwrite the search patten of filtlong in multiqc_config.yml
@jfy133
Merge pull request #535 from sofstam/documentation_release
81f39dd 
Update documentation to include db_type
@LilyAnderssonLee LilyAnderssonLee merged commit 6893894 into master Oct 3, 2024
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

@atrull314 atrull314 atrull314 approved these changes

@sofstam sofstam Awaiting requested review from sofstam

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@jfy133 @atrull314 @LilyAnderssonLee @sofstam @nf-core-bot