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

create subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer similar to nf-core/atacseq #401

Merged
merged 3 commits into from
Jul 9, 2024
Merged

create subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer similar to nf-core/atacseq #401

merged 3 commits into from
Jul 9, 2024

Conversation

bjlang
Copy link
Contributor

@bjlang bjlang commented Jul 8, 2024 •
edited

Third item of #398

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/chipseq 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).

@bjlang bjlang requested a review from JoseEspinosa July 8, 2024 12:12
@github-actions GitHub Actions
Copy link

github-actions bot commented Jul 8, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f4f8b68

+| ✅ 223 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-09 07:52:00

JoseEspinosa
JoseEspinosa requested changes Jul 8, 2024
View reviewed changes
Copy link
Member

@JoseEspinosa JoseEspinosa left a comment

Choose a reason for hiding this comment

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

Nice! only some minor questions/suggestions

conf/modules.config Outdated Show resolved Hide resolved
subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf Outdated Show resolved Hide resolved
subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf Outdated Show resolved Hide resolved
@bjlang bjlang requested a review from JoseEspinosa July 9, 2024 10:02
JoseEspinosa
JoseEspinosa approved these changes Jul 9, 2024
View reviewed changes
Copy link
Member

@JoseEspinosa JoseEspinosa left a comment

Choose a reason for hiding this comment

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

LGTM!

@JoseEspinosa JoseEspinosa merged commit a1dd9c2 into nf-core:dev Jul 9, 2024
9 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@JoseEspinosa JoseEspinosa JoseEspinosa 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.

None yet
2 participants
@bjlang @JoseEspinosa