Add SigProfilerMatrixGenerator

[FerriolCalvet]

Add SigProfilerMatrixGenerator to get DBS and ID matrices with the filtered mutations and also some simple plots.

Tested

AI summary

This pull request introduces new modules for mutational signature analysis and integrates them into the main workflow. The key changes are the addition of MAF_2_VCF and SIGPROFILER_MATRIXGENERATOR processes, their configuration and wiring in the pipeline, and the removal of the deprecated MSIGHDP process. There are also some cleanups and reorganization in the workflow files.

New modules and integration for mutational signature analysis:

• Added the MAF_2_VCF process to convert MAF files to VCF format, including Docker container specification, input/output handling, and version reporting (modules/local/maf2vcf/main.nf).
• Added the SIGPROFILER_MATRIXGENERATOR process for generating mutational signature matrices from VCF files, with support for multiple output types and genome assemblies (modules/local/signatures/sigprofiler/matrixgenerator/main.nf).
• Integrated MAF_2_VCF and SIGPROFILER_MATRIXGENERATOR into the main workflow, wiring their inputs and outputs and updating the pipeline logic to support signature analysis (workflows/deepcsa.nf) [1] [2] [3].

Configuration updates for new processes:

• Added configuration blocks for MAF2VCF and SIGPROMATRIXGENERATOR in conf/modules.config, specifying arguments and publish directories [1] [2].

Deprecation and cleanup:

• Removed the deprecated MSIGHDP process and its references from the codebase, including subworkflow and workflow files (modules/local/signatures/msighdp/main.nf, subworkflows/local/signatures/main.nf, subworkflows/local/signatures_hdp/main.nf) [1] [2] [3] [4] [5].

Workflow and code organization:

• Cleaned up and reorganized workflow files for clarity, including import order and comments (workflows/deepcsa.nf) [1] [2].

These changes collectively modernize and extend the pipeline's signature analysis capabilities while removing unused legacy code.

[Copilot]

Pull Request Overview

This pull request introduces new mutational signature analysis capabilities by adding SigProfilerMatrixGenerator integration and removes deprecated components. The main purpose is to modernize the signature analysis workflow with more robust matrix generation tools.

• Add MAF to VCF conversion and SigProfilerMatrixGenerator processes for comprehensive signature matrix generation
• Remove deprecated MSIGHDP process and related HDP signature extraction components
• Reorganize workflow imports and clean up code structure

Reviewed Changes

Copilot reviewed 7 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Integrates new MAF2VCF and SIGPROMATRIXGENERATOR processes, reorganizes imports
modules/local/maf2vcf/main.nf	New process to convert MAF files to VCF format
modules/local/signatures/sigprofiler/matrixgenerator/main.nf	New process for generating signature matrices using SigProfilerMatrixGenerator
modules/local/signatures/msighdp/main.nf	Removes deprecated MSIGHDP process
subworkflows/local/signatures/main.nf	Removes MSIGHDP references and commented code
subworkflows/local/signatures_hdp/main.nf	Cleans up commented code in HDP workflow
conf/modules.config	Adds configuration for new MAF2VCF and SIGPROMATRIXGENERATOR processes

Comments suppressed due to low confidence (1)

modules/local/signatures/sigprofiler/matrixgenerator/main.nf:1

• The command construction lacks proper quoting around variables that could contain spaces or special characters. Consider wrapping variables like ${prefix}, ${genome}, and ${args} in quotes to prevent issues with special characters.

process SIGPROFILER_MATRIXGENERATOR {

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