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

DRAFT: Extending output from snpEff #639

Merged
merged 4 commits into from
Jul 16, 2022
Merged

DRAFT: Extending output from snpEff #639

merged 4 commits into from
Jul 16, 2022

Conversation

asp8200
Copy link
Contributor

@asp8200 asp8200 commented Jul 16, 2022 •
edited
Loading

The purpose of this PR is just to include a summary-html-file and a genes-txt-file in the published output from snpEff.

Tests and git_sha of snpeff in modules.json have been updated.

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
Copy link
Contributor

looks good only thing missing is updating the module in nf-core/modules :)

asp8200 and others added 2 commits July 16, 2022 13:23
@asp8200 @FriederikeHanssen
Update conf/modules.config
31ad062 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@asp8200
Updating git_sha for snpEff
1552dfd
@github-actions
Copy link

github-actions bot commented Jul 16, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1552dfd

+| ✅ 145 tests passed       |+
#| ❔   4 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: 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 2022-07-16 18:25:22

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review July 16, 2022 19:37
@FriederikeHanssen FriederikeHanssen merged commit 3138184 into nf-core:dev Jul 16, 2022
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

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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
@asp8200 @FriederikeHanssen