Skip to content

Add Autocycler subtool modules (subsample, compress, cluster, trim, resolve, combine) #9274

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
Open
wants to merge 10 commits into
base: master
Choose a base branch
from
Open

Add Autocycler subtool modules (subsample, compress, cluster, trim, resolve, combine) #9274

wants to merge 10 commits into from

Conversation

@dwells-eit
Copy link
Contributor

PR checklist

Adds modules for autocycler subtools to allow complete autocycler workflow for consensus bacterial assembly.

  • subsample
  • compress
  • cluster
  • trim
  • resolve
  • combine

As discussed here only the non-assembly steps are implemented, allowing users to use other modules to generate assemblies however they like.

Closes #9252

  • 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
  • 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

sguizard
sguizard approved these changes Oct 28, 2025
View reviewed changes
Copy link
Contributor

@sguizard sguizard left a comment

Choose a reason for hiding this comment

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

LGTM

SPPearce
SPPearce requested changes Oct 28, 2025
View reviewed changes
dwells-eit and others added 8 commits October 29, 2025 11:05
@dwells-eit
Add autocycler modules
8ff062f
@dwells-eit
Write tests for autocycler subsample
9aa4425
@dwells-eit
Add autocycler module tests
78ca649
@dwells-eit
Fix lintting errors
7fe8546 
- Correct meta.yml output
- tag all modules included in tests
- remove final TODOs
@dwells-eit
Harshil Alignment
9f72413
@dwells-eit @SPPearce
Remove channel view (used for debugging)
a9b290d 
Co-authored-by: Simon Pearce <[email protected]>
@dwells-eit @SPPearce
Make empty gzipped fastq file for subsample stub
1407e31 
Work around for nf-test bug with .fastq.gz files that aren't gzipped

Co-authored-by: Simon Pearce <[email protected]>
@dwells-eit
Fix random seed by default and change test data
af9a94e 
Use small cov2 readset for testing, set genome size very low to allow subsampling
@dwells-eit dwells-eit requested a review from SPPearce October 29, 2025 11:22
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@sguizard sguizard sguizard approved these changes

@SPPearce SPPearce Awaiting requested review from SPPearce

Requested changes must be addressed to merge this pull request.

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

new module: autocycler tools (subsample, compress, cluster, trim, resolve, combine)

3 participants

@dwells-eit @sguizard @SPPearce