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.

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

Simplify CSV export and posfile usage #96

Merged
merged 42 commits into from
Jul 11, 2024

Conversation

LouisLeNezet
Copy link
Collaborator

@LouisLeNezet LouisLeNezet commented Jul 3, 2024

Now the tsv.gz is no more necessary as it is generated directly from the legend file.
All csv export is also simplify with the usage of a dedicated function that is nf-tested (more test could / should be done ?)

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/phaseimpute 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).

@LouisLeNezet LouisLeNezet marked this pull request as draft July 3, 2024 17:45
@LouisLeNezet LouisLeNezet self-assigned this Jul 3, 2024
@LouisLeNezet LouisLeNezet added bug Something isn't working documentation Improvements or additions to documentation enhancement New feature or request and removed bug Something isn't working labels Jul 3, 2024
@LouisLeNezet LouisLeNezet added this to the v0.99.0 milestone Jul 3, 2024
@LouisLeNezet LouisLeNezet marked this pull request as ready for review July 5, 2024 14:01
@LouisLeNezet LouisLeNezet requested a review from atrigila July 5, 2024 14:18
@LouisLeNezet LouisLeNezet requested a review from atrigila July 10, 2024 17:26
Copy link
Collaborator

@atrigila atrigila left a comment

Choose a reason for hiding this comment

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

Looks good!

@LouisLeNezet LouisLeNezet merged commit 41e311a into nf-core:dev Jul 11, 2024
8 checks passed
@LouisLeNezet LouisLeNezet deleted the simplify branch October 1, 2024 13:12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
documentation Improvements or additions to documentation enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Move BCFTOOLS convert to vcf extract Simplify csv subworkflow generation
2 participants