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

Run modkit once + general changes to methylation subworkflow #451

Open
wants to merge 25 commits into
base: dev
Choose a base branch
from
Open

Run modkit once + general changes to methylation subworkflow #451

wants to merge 25 commits into from

Conversation

Schmytzi
Copy link
Collaborator

@Schmytzi Schmytzi commented Oct 30, 2024 •
edited
Loading

Closes #385.
Changes:

  • Added phased input to METHYLATION subworkflow
  • Only call modkit once, with parameters depending on whether phasing was run
  • Moved subworkflow to own its own directory
  • Added tests

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
  • 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).

Schmytzi
Schmytzi commented Oct 30, 2024
View reviewed changes
workflows/nallo.nf Outdated Show resolved Hide resolved
@Schmytzi Schmytzi marked this pull request as ready for review October 30, 2024 13:07
@Schmytzi Schmytzi requested a review from a team as a code owner October 30, 2024 13:07
@Schmytzi Schmytzi changed the title Run modkit once + general changes to methylayion subworkflow Run modkit once + general changes to methylation subworkflow Oct 30, 2024
fellen31
fellen31 reviewed Oct 30, 2024
View reviewed changes
Copy link
Collaborator

@fellen31 fellen31 left a comment

Choose a reason for hiding this comment

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

Nice, really improving the code 💪

subworkflows/local/methylation/main.nf Outdated Show resolved Hide resolved
subworkflows/local/methylation/main.nf Show resolved Hide resolved
subworkflows/local/utils_nfcore_nallo_pipeline/main.nf Show resolved Hide resolved
workflows/nallo.nf Show resolved Hide resolved
@Schmytzi
Only running modkit once (depending on phasing)
ee80510
@Schmytzi
Moved methylation subworkflow to own directory
845fdbe
@Schmytzi
Added tests
7410399
@Schmytzi
Fixed test failures
fe42813
@Schmytzi
Updated tests
ba1dc73
@Schmytzi
Added input to methylation call site
e0a4180
@Schmytzi
Renamed input channel 0
39ff79f
@Schmytzi
Fixed alignment
014ea32
@Schmytzi
Fixed workflow dependencies
6a1ba6e
@Schmytzi
Updated pipeline test snapshot
e16f526
@Schmytzi
Only importing modkit once, setting args in config
2b737b9
@Schmytzi
Merged calls to METHYLATION
ce3e96a
@Schmytzi
Corrected process names
c680508
@Schmytzi
Merge changelog
87ef6c1
@Schmytzi
Added parameters to methylation tests
997dee3
@Schmytzi
Removed input phased
af8bb08
@Schmytzi
Added files to workflow output
0699445
@Schmytzi
Moved parameter check to methylation callsite
c3cd34c
@Schmytzi
Fixed test config
3ec358d
@Schmytzi
Fixed WhatsHap stats stub
15a4a4c
@Schmytzi
Fixed process selectors in test config
bf0b925
@Schmytzi
Fixed join in test
e76026a
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@fellen31 fellen31 Awaiting requested review from fellen31

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
Nallo
Status: No status
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Only run modkit once
2 participants
@Schmytzi @fellen31