Thanks to visit codestin.com
Credit goes to Github.com

Skip to content

Dev update #85

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
Merged
ferenckata merged 37 commits into from
Dec 3, 2025
Merged

Dev update #85

ferenckata merged 37 commits into from
Dec 3, 2025

Conversation

@ferenckata
Copy link

@ferenckata ferenckata commented Dec 3, 2025

Start updating and fixing current dev (nf-core version of cageflow)

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • 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/cageseq 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).
  • 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).

Sviatoslav Sidorov and others added 30 commits November 11, 2025 18:04
Added test maponly yamls and fixed SAMTOOLS_PROCESSING inclusion
eeef4fe
Fixed params schema
f8e17e4
Replaced SAMTOOLS() with SAMTOOLS_PROCESSING()
645b743
Removed sessionInfo from version printing
fa34b3a
Fixed apostrophes and added versions of ChIPseeker and CAGEfightR
9a3c660
Tested full+STAR+SE
ea18c61
Renamed full+STAR+SE yaml
d14ab42
Tested bowtie2 and star on PE, full pipeline
6e8e350
Tested maponly with defaul params
af54701
@ferenckata
fix schema
7f4ee14
@ferenckata
Merge branch 'dev' into test-and-fix-dev
ea0f672
@ferenckata
follow template for readme/ usage and docs
b64aef6
@ferenckata
Merge pull request #123 from ComputationalRegulatoryGenomicsICL/test-…
e953fc4 
…and-fix-dev

Test and fix dev - will continue developing here and merging regularly until it is all good
@ferenckata
sentence fix to open new pr and see ci
6a89fe0
@ferenckata
fixing two nf-core issues
c48a54c
@ferenckata
updated modules
bca360e
@ferenckata
ran nf-core tool to fix tests
bb5a0ed
@ferenckata
updated modules
78a8ac5
@ferenckata
more autofix creating more issues
9bf6287
@ferenckata
more autotest, one thing got actually fixed
001af21
@ferenckata
fix with pettier
363e495
@ferenckata
remove two failing files, lets see if that's a bigger problem
ffa8f5b
@ferenckata
template branch doesnt do anything, manually adding line to readme
683210c
@ferenckata
Template update for nf-core/tools version 3.3.2
4021821
@ferenckata
run linting
c0dc470
@ferenckata
remove log files for docker
2675d3c
@ferenckata
possibly wrong merging fixed
2f9b3ac
@ferenckata
remaining merge conflicts
587f327
@ferenckata
more updates
3c1ee12
@ferenckata
fix params hopefully
0692e08
@nf-core-bot
Copy link
Member

nf-core-bot commented Dec 3, 2025 •
edited
Loading

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@mashehu
Copy link
Contributor

mashehu commented Dec 3, 2025

@nf-core-bot fix linting

@ferenckata ferenckata merged commit 0e9e11e into dev Dec 3, 2025
5 of 11 checks passed
@ferenckata ferenckata deleted the dev-update branch December 3, 2025 11:02
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

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

@ferenckata @nf-core-bot @mashehu