Skip to content

Umi test#614

Merged
FriederikeHanssen merged 31 commits intonf-core:devfrom
WackerO:umi
Jul 17, 2022
Merged

Umi test#614
FriederikeHanssen merged 31 commits intonf-core:devfrom
WackerO:umi

Conversation

@WackerO
Copy link
Copy Markdown
Contributor

@WackerO WackerO commented Jul 1, 2022 •
edited by FriederikeHanssen
Loading

This PR gets the umi test running -->but not in pytest! nextflow run main.nf -profile test,umi,docker works, but the ci.yml tag for umi is commented out atm to make all tests pass.

close #611

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).

FriederikeHanssen
FriederikeHanssen reviewed Jul 1, 2022
View reviewed changes
Comment thread conf/modules.config Outdated
FriederikeHanssen
FriederikeHanssen reviewed Jul 1, 2022
View reviewed changes
Comment thread modules/nf-core/modules/samtools/view/main.nf Outdated
FriederikeHanssen
FriederikeHanssen reviewed Jul 1, 2022
View reviewed changes
Comment thread modules/nf-core/modules/samtools/view/main.nf Outdated
FriederikeHanssen
FriederikeHanssen reviewed Jul 1, 2022
View reviewed changes
Comment thread conf/modules.config
@WackerO WackerO marked this pull request as ready for review July 4, 2022 12:54
@github-actions
Copy link
Copy Markdown

github-actions Bot commented Jul 4, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eb07bf0

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-17 14:45:54

@WackerO WackerO marked this pull request as draft July 11, 2022 12:47
@WackerO WackerO marked this pull request as draft July 11, 2022 12:47
maxulysse
maxulysse reviewed Jul 11, 2022
View reviewed changes
Comment thread modules/nf-core/modules/fgbio/fastqtobam/main.nf Outdated
maxulysse
maxulysse reviewed Jul 11, 2022
View reviewed changes
Comment thread conf/modules.config
@WackerO WackerO marked this pull request as ready for review July 13, 2022 15:50
@WackerO WackerO mentioned this pull request Jul 15, 2022
Merged
14 tasks
@FriederikeHanssen FriederikeHanssen merged commit e8d484f into nf-core:dev Jul 17, 2022
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 17, 2022
Closed
2 tasks
@WackerO WackerO deleted the umi branch July 27, 2022 09:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@maxulysse maxulysse maxulysse left review comments

@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.

3 participants

@WackerO @maxulysse @FriederikeHanssen
⚡