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v1.2.1 - Bouncy Basenji Patch PR #554

Merged
merged 45 commits into from
Nov 28, 2024
Merged

v1.2.1 - Bouncy Basenji Patch PR #554

merged 45 commits into from
Nov 28, 2024

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sofstam
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@sofstam sofstam commented Nov 25, 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).

sofstam and others added 30 commits October 3, 2024 13:51
@sofstam
Update changelog after release
cfcc93a
@sofstam
Prettier
14d84e1
@sofstam
Merge pull request #538 from sofstam/bump_post_release
4cb0d37 
Bump up the version number after 1.2 release
@jfy133
Merge branch 'master' into dev
4418327
@nf-core-bot
Template update for nf-core/tools version 3.0.0
79d1535
@nf-core-bot
Template update for nf-core/tools version 3.0.1
56e023f
@nf-core-bot
Template update for nf-core/tools version 3.0.2
69969cf
@LilyAnderssonLee
resolve the conflicts
226abd9
@LilyAnderssonLee
remove max_cpu from test.config
ff4d28f
@LilyAnderssonLee
update schema wit new release
f3ef6aa
@LilyAnderssonLee
add exists:true to the sechma to check the file path
5e90741
@LilyAnderssonLee
change db_path format back to the original value path in schema_database
a9af810
@LilyAnderssonLee
update the type of run_accession into string and integer
9e20ff1
@LilyAnderssonLee @jfy133
Update CITATIONS.md
88c9f46 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee @jfy133
Update conf/modules.config
2900ae2 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee
address comments from James
b0c1154
@LilyAnderssonLee @jfy133
Update nextflow.config
340b0af 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee
Add Lili as co-author
05b743f
@jfy133
Fix CI to run each test separately
fb38fb7
@LilyAnderssonLee @jfy133
Update main.nf
353188d 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee @jfy133
Update .nf-core.yml
f7c6176 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@nf-core-bot
[automated] Fix code linting
dbabb5d
@jfy133
Fix mOTUs if/else statemetn
fe84cc3
@LilyAnderssonLee
update configs and database schema
00067f5
@LilyAnderssonLee
Merge pull request #545 from nf-core/nf-core-template-merge-3.0.2
e34437b 
Important! Template update for nf-core/tools v3.0.2
@jfy133
Add darkmode version of metromap
8262e0a
@jfy133
Merge pull request #548 from nf-core/darkmode-diagram
93aa499 
Add darkmode version of metromap
@jfy133
Fix darkmode diagram
6c6cd8c
@Midnighter
refactor: prepare the additional prefixes input
2e6f37d 
The KrakenUniq module has a breaking change requiring a further input.
@Midnighter
chore: update krakenuniq/preloadedkrakenuniq
a1a8289
Midnighter and others added 12 commits November 6, 2024 10:16
@Midnighter
fix: create always unique prefix
c0311a1
@Midnighter
fix: make prefix unique across PE and SE
30fc22a 
In the rare case that there are two samples with the same identifier and
run accession, one being single-end and the other paired-end, this
change makes the prefix and thus the KrakenUniq output filenames unique.
@jfy133
Update CHANGELOG.md
163d600
@jfy133
Merge pull request #549 from nf-core/darkmode-diagram
b2cac44 
Add darkmode diagram
@jfy133
Update CHANGELOG.md
3022cd2
@jfy133
Merge pull request #550 from nf-core/update-krakenuniq
e58a59c 
Update krakenuniq
@LilyAnderssonLee
update nonpareil/curve
51b8acb
@LilyAnderssonLee
update CHANGELOG.md
4da7342
@LilyAnderssonLee
Merge pull request #552 from nf-core/nonpareil_curve_update
7d261e8 
update the module nonpareil/curve
@LilyAnderssonLee
bump the version
716dd78
@LilyAnderssonLee
update changelog
42479b0
@LilyAnderssonLee
Merge pull request #553 from nf-core/pre_patch_bump_v
1a27aaa 
Bump the version before patch release v 1.2.1
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github-actions bot commented Nov 25, 2024 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit acd85cc

+| ✅ 283 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-28 09:55:33

LilyAnderssonLee
LilyAnderssonLee approved these changes Nov 26, 2024
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LGTM!

LouisLeNezet
LouisLeNezet requested changes Nov 26, 2024
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Nice work !
I don't really know what this pipeline do but it seems solid.
On a global scale, it would be nice to add some nf-test on the local modules/subworkflows and on the whole pipeline to follow the modification and their impact ;)
But that can be done on another release as it is quite the work.

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@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Nov 27, 2024
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LilyAnderssonLee commented Nov 27, 2024 •
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Nice work ! I don't really know what this pipeline do but it seems solid. On a global scale, it would be nice to add some nf-test on the local modules/subworkflows and on the whole pipeline to follow the modification and their impact ;) But that can be done on another release as it is quite the work.

Yes, we are planning to do that in the next release. The issue has been created: #555

@LilyAnderssonLee
Merge pull request #556 from nf-core/patch_release_fix
acd85cc 
Address review comments for Patch release v1.2.1
@LilyAnderssonLee LilyAnderssonLee merged commit 0af416a into master Nov 28, 2024
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

@LouisLeNezet LouisLeNezet LouisLeNezet approved these changes

@jfy133 jfy133 jfy133 left review comments

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6 participants
@sofstam @LilyAnderssonLee @jfy133 @LouisLeNezet @nf-core-bot @Midnighter