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Dev => Master 2.3.0#185

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edmundmiller merged 279 commits into
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May 7, 2025
Merged

Dev => Master 2.3.0#185
edmundmiller merged 279 commits into
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@edmundmiller edmundmiller commented Dec 23, 2024 •
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Waiting for #184

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/nascent 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).

edmundmiller and others added 30 commits April 25, 2024 17:28
@edmundmiller
test: Write basic STAR test
ca68e9b
@edmundmiller
fix: Make sure the gtf is unzipped
9940414
@edmundmiller
docs: Add info about the sample column concatinating group and replic…
3d4db1d 
…ate columns
@edmundmiller
refactor: Pass bais to transcript identification for PINTS
c49e9d7
@edmundmiller
feat: Bump CHM13 fasta
2aeb303
@edmundmiller
fix: Update CHM13
63f5074
@edmundmiller
chore: Update CHANGELOG
4bd6a11
@edmundmiller @maxulysse
build: Add params.human-pandgenomics_base
c47db7e 
Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>
@edmundmiller
Merge pull request #142 from nf-core/STAR
9561941 
Add STAR aligner
@nf-core-bot @edmundmiller
Template update for nf-core/tools version 2.14.0
25f8d5d
@nf-core-bot @edmundmiller
Template update for nf-core/tools version 2.14.1
5522aab
@edmundmiller
style: Try to fix linting
25d8803
@edmundmiller
build: Remove extra "groseq" workflow
0280009
@edmundmiller
chore: nf-core modules update
47ba2f4
@edmundmiller
fix: Catch up with module updates
64acae7
@edmundmiller
chore: nf-core modules update subworkflow
ed8510f
@edmundmiller
ci: Bump detect-nf-test-changes to 0.0.3
45455b6
@edmundmiller
style: Fix CI triggers
f41ddfd 
https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_ci
@edmundmiller
style: Minimum pipeline NF version
9226907 
https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_ci
@edmundmiller
style: Ignore ci.yml
1582d2b
@edmundmiller
chore: nf-core subworkflows update
f5ae7ff
@edmundmiller
style: Remove stray comment update
2801dea
@edmundmiller
test: Update snapshot for GitHub actions
cc8cc7e
@edmundmiller
test: Skip preseq in BWA test
0319bc1 
#148
@edmundmiller
Merge pull request #147 from nf-core/update-modules
9954adf 
Update Modules
@edmundmiller
chore: Add citations
93c5d37
@edmundmiller
Merge pull request #149 from nf-core/doi
f5f9620 
Add citations to MultiQC
@edmundmiller
chore: Update naming
73aad31
@edmundmiller
chore(homer): Fix errors about unexpected input tuple size
bce004d
@edmundmiller
Merge pull request #151 from nf-core/homer-inputs
6592199 
Fix HOMER inputs
maxulysse
maxulysse reviewed Apr 23, 2025
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Comment thread CHANGELOG.md
maxulysse
maxulysse reviewed Apr 23, 2025
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Comment thread modules/local/grohmm/parametertuning/main.nf
maxulysse
maxulysse reviewed Apr 23, 2025
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Comment thread tests/lib/UTILS.groovy Outdated
maxulysse
maxulysse reviewed Apr 23, 2025
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Comment thread nf-test.config Outdated
maxulysse
maxulysse requested changes Apr 23, 2025
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Minor comments

@edmundmiller @maxulysse
chore: Update nf-test.config triggers and remove unused UTILS class
31f35f7 
Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>
@edmundmiller edmundmiller requested a review from maxulysse April 24, 2025 03:49
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maxulysse commented Apr 24, 2025

You have a couple of issues with the snapshots.
I would recommend to update the GHA to make it so that we can see more clearly which tests are failing, and properly differentiate the different tests that are being run

maxulysse
maxulysse reviewed May 4, 2025
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Comment thread CITATIONS.md
maxulysse
maxulysse approved these changes May 4, 2025
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Minor issues with conda and download, but LGTM

maxulysse
maxulysse reviewed May 5, 2025
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Comment thread CITATIONS.md
maxulysse
maxulysse reviewed May 5, 2025
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Comment thread docs/output.md
maxulysse
maxulysse approved these changes May 5, 2025
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minor comments, ok for me

@edmundmiller edmundmiller merged commit 7d4fe61 into master May 7, 2025
38 of 44 checks passed
@github-project-automation github-project-automation Bot moved this from In Progress to Done in PRs to master May 7, 2025
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@maxulysse maxulysse maxulysse approved these changes

@sateeshperi sateeshperi sateeshperi approved these changes

@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas

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@edmundmiller @maxulysse @vagkaratzas @sateeshperi @nf-core-bot