modules

modules copied to clipboard

## WARNING - [ ] I have made sure to update the singularity and conda images This PR contains the following updates: | Package | Update | Change | |---|---|---|...

renovate[bot]

## PR checklist Closes #8165 - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

giorgiagandolfi

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

giorgiagandolfi

[FEATURE] Update modules to remove undocumented task.ext fields

1

### Is your feature request related to a problem? Please describe task.ext fields were introduced allow users to override developer settings in pipelines. However some modules are simply using them...

mahesh-panchal

Adding CNAqc module https://caravagnalab.github.io/CNAqc/ ## PR checklist Closes #8610 - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or...

vvvirgy

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

vmelichar

## PR checklist Closes #XXX - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

famosab

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

Y-Pei

Added braker3

5

Closes #6034 Added braker3

GallVp

feat: support no reference tumor only cnvkit analysis

3

> [!NOTE] > The failing tests on this PR are only occurring with nextflow=24.10.2 for a single stub test and are due to a known nextflow bug, https://github.com/nextflow-io/nextflow/issues/5456 The `cnvkit/batch`...

znorgaard