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 parsing of GTDB-Tk version #307

Merged
merged 4 commits into from
May 30, 2022
Merged

Fix parsing of GTDB-Tk version #307

merged 4 commits into from
May 30, 2022

Conversation

skrakau
Copy link
Member

@skrakau skrakau commented May 28, 2022 •
edited
Loading

Fix parsing of GTDB-Tk version: only process first line, i.e. avoid new line containing "Note: There is a newer version of GTDB-Tk available: v2.1.0". Caused error in CUSTOM_DUMPSOFTWAREVERSIONS.

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/mag 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).

@github-actions
Copy link

github-actions bot commented May 28, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dc3b065

+| ✅ 147 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-05-30 12:10:00

@skrakau skrakau requested a review from d4straub May 29, 2022 18:51
d4straub
d4straub approved these changes May 30, 2022
View reviewed changes
Copy link
Collaborator

@d4straub d4straub left a comment

Choose a reason for hiding this comment

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

LGTM!

@skrakau skrakau merged commit b5fcdc9 into nf-core:dev May 30, 2022
@skrakau skrakau deleted the fix_gtdbtk_version_retrieval branch July 22, 2022 09:24
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@d4straub d4straub d4straub 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
@skrakau @d4straub