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

Add chunk_model as parameter #157

Merged
merged 7 commits into from
Nov 10, 2024
Merged

Conversation

LouisLeNezet
Copy link
Collaborator

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 pipelines 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 self-assigned this Nov 8, 2024
@LouisLeNezet LouisLeNezet added the enhancement New feature or request label Nov 8, 2024
@LouisLeNezet LouisLeNezet added this to the v0.99.0 milestone Nov 8, 2024
@LouisLeNezet
Copy link
Collaborator Author

I've retried on my cluster and the fulltest does now work without any issue with the modification on GLIMPSE2_chunk.

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.

The idea is good, some tests are missing in order to use sequential as the default chunk model for the pipeline. We should assert that it really works, otherwise, we will have the same problem when testing with AWS mega tests.

nextflow.config Show resolved Hide resolved
nextflow_schema.json Outdated Show resolved Hide resolved
subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test Outdated Show resolved Hide resolved
conf/steps/panel_prep.config Show resolved Hide resolved
workflows/phaseimpute/main.nf Outdated Show resolved Hide resolved
@LouisLeNezet LouisLeNezet merged commit 06d6b60 into nf-core:dev Nov 10, 2024
12 checks passed
@LouisLeNezet LouisLeNezet deleted the chunk_model branch November 18, 2024 12:41
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants