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

fix cardinality when params.bowtie2_index used #439

Merged
merged 5 commits into from
Aug 27, 2024
Merged

fix cardinality when params.bowtie2_index used #439

merged 5 commits into from
Aug 27, 2024

Conversation

Joon-Klaps
Copy link

@Joon-Klaps Joon-Klaps commented Aug 26, 2024 •
edited
Loading

PR checklist

When given bowtie2_index from a param, it is read in as a value channel but when constructed from bowtie2 build it's a
[ [:] , path(bowtie2/index/) ]. Meaning it's missing the meta.

  • 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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions GitHub Actions
Copy link

github-actions bot commented Aug 26, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 828c52d

+| ✅ 190 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 247]

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-26 15:33:38

@Joon-Klaps Joon-Klaps requested a review from svarona August 26, 2024 11:17
@Joon-Klaps
Copy link
Author

Fixes #440

@Joon-Klaps Joon-Klaps mentioned this pull request Aug 26, 2024
Closed
svarona
svarona approved these changes Aug 27, 2024
View reviewed changes
Copy link
Contributor

@svarona svarona left a comment

Choose a reason for hiding this comment

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

LGTM!

@Joon-Klaps Joon-Klaps merged commit c293787 into dev Aug 27, 2024
25 checks passed
@Joon-Klaps Joon-Klaps deleted the bowtie-index-cardinality branch August 27, 2024 08:02
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@svarona svarona svarona 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.
2 participants
@Joon-Klaps @svarona