Skip to content

fix large assemblies#236

Merged
d4straub merged 3 commits intonf-core:devfrom
d4straub:dev
Oct 20, 2021
Merged

fix large assemblies#236
d4straub merged 3 commits intonf-core:devfrom
d4straub:dev

Conversation

@d4straub
Copy link
Copy Markdown
Collaborator

@d4straub d4straub commented Oct 19, 2021 •
edited
Loading

This should solve #235

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!
  • 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
Copy Markdown

github-actions Bot commented Oct 19, 2021 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b49357d

+| ✅ 136 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-10-20 09:46:01

FriederikeHanssen
FriederikeHanssen approved these changes Oct 19, 2021
View reviewed changes
Copy link
Copy Markdown
Contributor

@FriederikeHanssen FriederikeHanssen left a comment

Choose a reason for hiding this comment

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

LGTM

@d4straub
Copy link
Copy Markdown
Collaborator Author

d4straub commented Oct 20, 2021

centrifuge --version | head -n 1 | sed 's/^.*centrifuge-class version //' > ${software}.version.txt led in some environments to errors:

(ERR): centrifuge-class died with signal 13 (PIPE)

I replaced it with centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //' > ${software}.version.txt

@d4straub
Copy link
Copy Markdown
Collaborator Author

d4straub commented Oct 20, 2021

Thanks for the review!

@d4straub d4straub merged commit d63ce61 into nf-core:dev Oct 20, 2021
@d4straub d4straub mentioned this pull request Oct 25, 2021
Merged
10 tasks
@d4straub d4straub mentioned this pull request May 30, 2022
Merged
10 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen 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

@d4straub @FriederikeHanssen