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

Allow sorting inputs to SVDB #6794

Merged
merged 5 commits into from
Oct 18, 2024
Merged

Conversation

fellen31
Copy link
Contributor

@fellen31 fellen31 commented Oct 17, 2024

This PR adds functionality for sorting the input files to SVDB. This allows the output to be snapshot when this module is included in a subworkflow, since the sample order in the output files will be fixed. The priority tags are sorted together with the VCFs, so the priority order is unchanged.

It also adds a check to make sure there are as many priority tags as input VCFs.

Tests should cover all usages.

PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@fellen31 fellen31 marked this pull request as ready for review October 17, 2024 09:35
Copy link
Contributor

@ramprasadn ramprasadn left a comment

Choose a reason for hiding this comment

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

LGTM! Can you just add a note saying that the order of the vcf files should correspond to the values in the priority channel? I should have done that when I first added the module, but better late than never 😄

@fellen31
Copy link
Contributor Author

Thanks! I think it was already in there, but I clarified the meta.

@fellen31 fellen31 added this pull request to the merge queue Oct 18, 2024
Merged via the queue into nf-core:master with commit b80931c Oct 18, 2024
12 checks passed
@fellen31 fellen31 deleted the fix-svdb-merge branch October 18, 2024 07:43
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants