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

3 - Write background list #245

Merged
merged 2 commits into from
Jul 22, 2024
Merged

3 - Write background list #245

merged 2 commits into from
Jul 22, 2024

Conversation

WackerO
Copy link
Collaborator

@WackerO WackerO commented Jul 19, 2024 •
edited
Loading

Added background list to output for reproducibility, removed hard-coded gprofiler DBs from report.
Also slightly changed the report text that shows when the gprofiler GMT file could not be downloaded so that it integrates better into the surrounding text.
This PR directly raises the pipeline version to 2.4 instead of setting it to dev as I will release after this PR

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
  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Jul 19, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 34af7c2

+| ✅ 172 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-22 10:34:47

@skrakau skrakau self-requested a review July 19, 2024 09:29
@skrakau
Copy link
Collaborator

skrakau commented Jul 19, 2024

Hi Oskar, could you generate separate commits and PRs for different topics? It greatly facilitates reviewing and maintenance, i.e. traceability of changes. For example, a separate PR for the version changes, and separate commits for the different changes in the report.

skrakau
skrakau reviewed Jul 19, 2024
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
@WackerO WackerO changed the title Write background list 3 - Write background list Jul 19, 2024
skrakau
skrakau approved these changes Jul 22, 2024
View reviewed changes
Copy link
Collaborator

@skrakau skrakau left a comment

Choose a reason for hiding this comment

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

LGTM! :)

@WackerO WackerO merged commit df4c728 into qbic-pipelines:dev Jul 22, 2024
16 checks passed
@WackerO WackerO deleted the write_bg_list branch July 22, 2024 11:28
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@skrakau skrakau skrakau 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
@WackerO @skrakau