Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Release 1.5.0 #256

Merged
merged 226 commits into from
May 8, 2024
Merged

Release 1.5.0 #256

merged 226 commits into from
May 8, 2024

Conversation

WackerO
Copy link
Collaborator

@WackerO WackerO commented Mar 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/differentialabundance 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).

WackerO and others added 30 commits October 31, 2023 18:35
@WackerO
Added round param for all modules (currently active for proteus und g…
8f537bf 
…profiler), added citations for gprofiler, added gprofiler section to report
@WackerO
Merge branch 'dev' of https://github.com/nf-core/differentialabundance …
5c203cc 
…into add_gpro
@WackerO
Param rename, reordered Citations, changed gprofiler2 report heading,…
1b891c5 
… added report text if no enrichment found, added gprofiler2 params to report and nextflow schema
@WackerO
Added docs entry for gprofiler
dbb7355
@WackerO
Corrected some entries in the schema
a0797b7
@WackerO
integrated module changes
0af6ce1
@WackerO
Added PI and contact params for report; added newline between report …
8ae788f 
…author and workflow version
@WackerO
Newly installed gprofiler2 module, enabled it in full test
f7e2f7e
@WackerO
Merge branch 'dev' of https://github.com/nf-core/differentialabundance …
454c23c 
…into add_gpro
@WackerO
added gprofiler to git
c7b93fc
@WackerO
prettier
ac07d6e
@WackerO
Added gpro to test.config
52a5d08
@WackerO
changing the workflow to make gprofiler run multiple times if several…
d72f277 
… contrasts are investigated
@WackerO
Merge branch 'dev' of https://github.com/nf-core/differentialabundance …
c289494 
…into add_gpro
@WackerO
GOST module update
a0f7ab1
@WackerO
Merge branch 'dev' of https://github.com/nf-core/differentialabundance …
786ec25 
…into add_gpro
@WackerO
Merge branch 'dev' of https://github.com/nf-core/differentialabundance …
f1205c5 
…into add_gpro
@WackerO
Removed write statements, updated metro map
0df5a89
@WackerO
Corrected metro maps, uncommented error case in workflow, fixed spell…
68695b7 
…ing error in schema, added rds to GOST output
@pinin4fjords
bump versions
5b7441b
@pinin4fjords
Fix resource issues
c0c4de6
@pinin4fjords
update changelog
c993eac
@nf-core-bot
[automated] Fix linting with Prettier
2b2caae
@pinin4fjords
Update changelog
3f56135
@pinin4fjords
Merge branch 'de_resources' of github.com:nf-core/differentialabundan…
804d6e5 
…ce into de_resources
@pinin4fjords
Merge pull request #208 from nf-core/de_resources
f09a2fc 
Fix resource issues and bump versions
@WackerO
Added filtered DE tables to output; add rounding after gprofiler2 PR …
0a24c7c 
…is merged
@WackerO
Renamed round_digits to report_round_digits, excluded gsea from defau…
ffbae15 
…lt report params
@WackerO
Merge branch 'dev' of https://github.com/nf-core/differentialabundance …
57f83b8 
…into add_gpro
@WackerO
fixed schema, added icons to proteus and gprofiler2
ced9196
maxulysse
maxulysse reviewed May 7, 2024
View reviewed changes
docs/images/workflow.png Outdated Show resolved Hide resolved
maxulysse
maxulysse reviewed May 7, 2024
View reviewed changes
main.nf Outdated Show resolved Hide resolved
maxulysse
maxulysse reviewed May 7, 2024
View reviewed changes
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looking good, minor comments

pinin4fjords
pinin4fjords approved these changes May 8, 2024
View reviewed changes
Copy link
Member

@pinin4fjords pinin4fjords left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Nice, looking good- think I reviewed all the component PRs in some detail anyway.

Adding my approval so you don't need to wait later, but you'll have to PR Maxime's points to dev to get them in (the branch protections are what prevent you from applying them here).

@WackerO WackerO requested a review from maxulysse May 8, 2024 10:34
@WackerO WackerO merged commit 3dd360f into master May 8, 2024
25 checks passed
@WackerO
Copy link
Collaborator Author

WackerO commented May 8, 2024

Many thanks you two!

@WackerO WackerO mentioned this pull request Jul 4, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@pinin4fjords pinin4fjords pinin4fjords approved these changes

@maxulysse maxulysse maxulysse approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@WackerO @maxulysse @pinin4fjords @nf-core-bot