Documenting and cleaning

[FerriolCalvet]

Human summary

• a bit of cleaning
• bump nextflow version to 25.04.2
• remove Ensembl VEP prepare cache step

AI generated summary

This pull request includes updates to the README.md file to enhance documentation and changes to configuration files to simplify and standardize file naming conventions. Below are the most important changes grouped by theme:

Documentation Updates

• Removed placeholder comments and added clearer instructions in README.md for preparing the samplesheet.csv file, detailing its required format and providing additional guidance on sample naming conventions.
• Updated the pipeline usage section in README.md to include the --input option for specifying the input file and added a note about configuring the -work-dir option.
• Added a new section in README.md to document expected file formats for inputs, with a reference to the assets/example_inputs directory.

Configuration Simplifications

• Standardized the ext.prefix values across multiple processes in conf/modules.config by removing the use of meta.id and replacing it with simplified naming conventions. For example, ${meta.id}.subset_depths was changed to .subset_depths. [1] [2] [3]
• Removed unused or redundant configuration blocks, such as conditions for params.indels, params.mutated_cells_vaf, and params.signatures. [1] [2] [3]

Tool-Specific Configurations

• Updated conf/tools/omega.config to align file naming conventions with the changes in conf/modules.config, simplifying ext.prefix values for processes like OMEGAMULTI and OMEGANONPROTMULTI.
• Removed unnecessary container configurations from conf/tools/panels.config for the VCFANNOTATEPANEL process, streamlining the configuration.

[Copilot]

Pull Request Overview

This PR cleans up redundant stub arguments across modules, renames and refactors the mutability process to “relative mutability,” and updates configuration closures and documentation for clarity.

• Removed unnecessary def args lines in many process stub sections to simplify module templates.
• Renamed COMPUTE_MUTABILITY to COMPUTE_RELATIVE_MUTABILITY and updated prefixes, patterns, and file outputs accordingly.
• Adjusted config closures to accept meta parameters and refined README with concrete usage examples and resolved placeholders.

Reviewed Changes

Copilot reviewed 61 out of 61 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
modules/local/computedepths/main.nf	Removed redundant def args in stub section
modules/local/compute_trinucleotide/main.nf	Cleaned stub args lines
modules/local/compute_profile/main.nf	Cleaned stub args lines
modules/local/compute_mutability/main.nf	Renamed process, updated outputs, removed stub args
modules/local/combine_sbs/main.nf	Removed stub args lines
modules/local/bbgtools/oncodrivefml/main.nf	Removed stub args in stub
modules/local/bbgtools/oncodriveclustl/main.nf	Removed stub args in stub
modules/local/bbgtools/oncodrive3d/run/main.nf	Removed stub args in stub
modules/local/bbgtools/oncodrive3d/preprocessing/main.nf	Removed stub args in script and stub
modules/local/bbgtools/oncodrive3d/plot_chimerax/main.nf	Tidied comments, removed stub args
modules/local/bbgtools/oncodrive3d/plot/main.nf	Removed stub args
modules/local/bbgtools/omega/preprocess/main.nf	Removed stub args
modules/local/bbgtools/omega/estimator/main.nf	Adjusted touch filename, removed stub args
modules/local/annotatedepth/main.nf	Removed stub args
main.nf	Removed preview setting and unused plugin import
conf/tools/panels.config	Cleaned blank lines in ext.args conditional block
conf/tools/omega.config	Updated ext.prefix closures to use meta ->
conf/modules.config	Refactored closures, removed commented blocks
README.md	Replaced placeholders with concrete examples; left some TODO markers

Comments suppressed due to low confidence (3)

modules/local/compute_mutability/main.nf:44

• The stub is touching ${prefix}.profile.json, but this process outputs *.relative_mutability_per_site.tsv. Update the stub to touch ${prefix}.relative_mutability_per_site.tsv (and adjusted variant) to reflect actual outputs.

touch ${prefix}.profile.json

README.md:2

• [nitpick] There are leftover TODO placeholders and comment markers in the README that may confuse users. Remove or resolve these sections to finalize documentation.

<!-- TODO nf-core:

conf/modules.config:42

• [nitpick] There are multiple large commented-out blocks in this config. Cleaning up or removing obsolete commented code will improve readability and maintainability.

// If just VEP: <vcf prefix>_VEP.ann.vcf

[FerriolCalvet]

lots of changes but seems like it should work

[Copilot]

Pull Request Overview

This PR focuses on cleaning up the code and updating documentation. Key changes include:

• Simplifying prefix assignment logic in multiple Nextflow processes.
• Removing unused variables and container logic.
• Updating the README and configuration files for clearer documentation and maintainability.

Reviewed Changes

Copilot reviewed 86 out of 86 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
modules/local/bbgtools/sitecomparison/main.nf	Simplified prefix assignment in both script and stub sections
modules/local/bbgtools/oncodrivefml/main.nf	Updated prefix transformation and removed redundant variable initialization
modules/local/bbgtools/oncodriveclustl/main.nf	Consistent update of prefix assignment in script and stub blocks
modules/local/bbgtools/oncodrive3d/*	Aligned prefix assignment changes across different process steps
modules/local/bbgtools/omega/*	Updated lambda expressions and prefix logic for improved consistency
conf/*	Removed outdated container assignments and simplified publishDir/prefix settings in configuration files
README.md	Updated usage examples and clarified input requirements

[FedericaBrando]

Nice cleaning Ferriol!

I added some minor comments and suggestions on what I saw in this PR. Good job! A step closer to a full production ready pipeline!

[FerriolCalvet]

ready to be merged to dev