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

Make target bed file optional for WGS mode #395

Merged
merged 5 commits into from
Aug 4, 2023
Merged

Make target bed file optional for WGS mode #395

merged 5 commits into from
Aug 4, 2023

Conversation

ramprasadn
Copy link
Collaborator

PR checklist

Fixes #375

  • 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/raredisease 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 --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@ramprasadn ramprasadn linked an issue Aug 1, 2023 that may be closed by this pull request
Pipeline in WGS mode appears to require target_bed #375
Closed
@github-actions
Copy link

github-actions bot commented Aug 1, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aea0b73

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-04 08:22:17

@ramprasadn ramprasadn marked this pull request as ready for review August 1, 2023 16:33
jemten
jemten approved these changes Aug 4, 2023
View reviewed changes
Copy link
Collaborator

@jemten jemten left a comment

Choose a reason for hiding this comment

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

good stuff

@ramprasadn ramprasadn merged commit ccd6a79 into nf-core:dev Aug 4, 2023
8 checks passed
@ramprasadn ramprasadn mentioned this pull request Aug 4, 2023
Closed
@ramprasadn ramprasadn deleted the update-config branch August 22, 2023 10:37
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jemten jemten jemten 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.

Pipeline in WGS mode appears to require target_bed
2 participants
@ramprasadn @jemten