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- we force the input to be provided with the AM fields in the VCF - not tested
- not tested
- define domains file in structural configs
- new mandatory param domains_file - update docs for domain and for features - expand regions handling with click
- in case AM not available we define the same as duplex
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Pull Request Overview
This pull request removes outdated project-specific configuration files and introduces new modular configuration modes to streamline the codebase. The changes include removing multiple project configurations, adding three new mode-based configurations, and updating parameter handling to use click-based command line interfaces.
- Removes 10+ project-specific configuration files that are no longer needed
- Adds three new modular configuration modes: basic, clonal_structure, and get_signatures
- Updates parameter handling to use click-based CLI with proper argument passing
- Introduces new required parameter for domain file specification
Reviewed Changes
Copilot reviewed 31 out of 34 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/deepcsa.nf | Simplifies DNDS workflow by moving parameter handling internally |
| subworkflows/local/mutatedcells/vaf/main.nf | Removes conditional logic around duplex counts processing |
| subworkflows/local/dnds/main.nf | Moves covariates and ref_trans parameter handling into the workflow |
| subworkflows/local/createpanels/main.nf | Updates domain file handling to use new domains_file parameter |
| nextflow_schema.json | Adds domains_file parameter and removes all_duplex_counts parameter |
| nextflow.config | Adds domains_file parameter and replaces project profiles with mode profiles |
| modules/local/vcf2maf/main.nf | Updates to use click-based CLI with proper argument structure |
| modules/local/expand_regions/main.nf | Updates to use click-based CLI for add_hotspots.py |
| modules/local/bbgtools/oncodrive3d/*/main.nf | Updates container reference and version handling |
| docs/usage.md | Documents new domains_file parameter requirement |
| docs/file_formatting.md | Adds documentation for domain definition file format |
| conf/test_real.config | Updates selected_genes parameter with actual gene list |
| conf/test.config | Removes all_duplex_counts parameter |
| conf/modules.config | Updates VCF2MAF configuration and VAF filtering logic |
| conf/modes/*.config | New modular configuration files for different analysis modes |
| conf/general_files_*.config | Adds domains_file parameter specification |
| conf/*.config (removed) | Removes multiple outdated project-specific configuration files |
FedericaBrando
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Jul 30, 2025
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FedericaBrando
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FedericaBrando
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Way cleaner the config part! Nice 🚀
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AI generated summary
This pull request removes outdated configuration files and introduces new configuration modes to streamline the codebase and improve modularity. The most important changes include the removal of several unused configuration files, the addition of new configuration modes, and updates to process parameters in existing configuration files.
Removal of outdated configuration files:
conf/bladder.config,conf/chip.config,conf/kidney.config,conf/lung.config,conf/mice_mm10.config, and others. These files contained parameters and processes no longer relevant to the current pipeline. [1] [2] [3] [4] [5] etc.)Addition of new configuration modes:
conf/modes/basic.configwith basic parameters for plotting depths, enabling signatures, and profiling all regions.conf/modes/clonal_structure.configwith parameters for mutation density, clonal structure analysis, and omega metrics.conf/modes/get_signatures.configwith parameters for mutation density, profiling non-protein coding regions, and extracting signatures.Updates to existing configuration files:
conf/general_files_BBG.configandconf/general_files_IRB.configto include a newdomains_fileparameter for oncodrive3d analysis. [1] [2]conf/modules.configto simplify and standardize process arguments, such as replacingext.levelwithext.argsand adjusting filters for VAF thresholds. [1] [2]These changes improve maintainability by removing obsolete configurations and introducing modular, reusable modes for specific analysis tasks. Let me know if you have any questions!