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

Add ampliseq samplesheet creation dependent on #790 in ampliseq #324

Draft
wants to merge 3 commits into
base: dev
Choose a base branch
from
Draft

Add ampliseq samplesheet creation dependent on #790 in ampliseq #324

wants to merge 3 commits into from

Conversation

jenmuell
Copy link

@jenmuell jenmuell commented Oct 29, 2024 •
edited
Loading

The code will be usable after the issue #790 in ampliseq will standardize the samplesheet.

I have added the following changes to support the automated creation of a samplesheet for ampliseq in fetchngs:

  • added custom columns for ampliseq in modules/local/sra_to_samplesheet/main.nf
  • added ampliseq flag to nextflow_schema.json
  • added test case for ampliseq: workflow/sra/tests/sra_nf_core_pipeline_ampliseq.nf.test

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/fetchngs 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Oct 29, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9c5ec43

+| ✅ 167 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-29 10:15:03

@jenmuell jenmuell self-assigned this Oct 29, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees

@jenmuell jenmuell

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@jenmuell @drpatelh