add plotting of profiles similarity

[FerriolCalvet]

• add generation of heatmaps to compare profiles between groups using cosine similarity

AI summary

This pull request introduces a new process for concatenating mutational profiles and integrates it into the existing mutational profiling workflow. The changes enable the aggregation of mutation profiles with group information and update the main workflow to support this functionality.

New process integration and workflow updates:

• Added a new CONCAT_PROFILES process in modules/local/concatprofiles/main.nf that aggregates mutation profiles and generates summary outputs, including heatmaps, clustermaps, cosine similarity tables, and compiled profiles.
• Integrated the CONCAT_PROFILES process into the MUTATIONAL_PROFILE subworkflow by importing it and updating the workflow to pass the required all_groups parameter and emit the compiled profiles output. [1] [2] [3]

Main workflow parameter and invocation changes:

• Updated the DEEPCSA workflow in workflows/deepcsa.nf to pass the new TABLE2GROUP.out.json_allgroups parameter to all mutational profile subworkflows, ensuring group information is available for profile aggregation. [1] [2]

[Copilot]

Pull Request Overview

This pull request adds functionality for plotting profile similarities and includes several improvements to the deepCSA pipeline configuration and documentation. The changes introduce new plotting capabilities, enhanced filtering options with Nanoseq masks, and improved process management.

• Added profile similarity plotting with heatmaps and clustering analysis
• Introduced Nanoseq mask filtering for SNPs and noisy genomic regions
• Enhanced group-based plotting capabilities with configurable options

Reviewed Changes

Copilot reviewed 44 out of 60 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Added group key extraction logic, updated mutation profile and plotting subworkflow calls to support group-based analysis
workflows/tests/deepcsa.nf.test	Added new workflow test for minimal features
subworkflows/local/mutationprofile/main.nf	Added profile concatenation and similarity analysis
subworkflows/local/mutationpreprocessing/main.nf	Implemented Nanoseq mask filtering for human samples
subworkflows/local/plottingsummary/main.nf	Added group-based plotting with configurable all-samples-only mode
subworkflows/local/omega/main.nf	Added QC evaluation for omega global/local estimation
modules/local/concatprofiles/main.nf	New module for concatenating profiles and computing similarity metrics
modules/local/plot/qc/globalloc_synonymous/main.nf	New module for omega synonymous QC plotting
modules/local/filterbed/main.nf	Enhanced filtering with positive/negative flag support
modules/local/plot/saturation/main.nf	Updated input parameters by combining site comparison with results
nextflow.config	Added plot_only_allsamples parameter and Nanoseq mask parameters
conf/modules.config	Added Nanoseq filtering process configurations
conf/general_files_IRB.config	Added Nanoseq mask file paths
conf/tmp_quick_fixes.config	Added error handling for specific processes
docs/usage.md	Added Nanoseq masks documentation section
docs/tools.md	New documentation explaining adjusted mutation density and other tools
test_data/modules/*.bed	Added test data files for PPM1D exons and domains

Comments suppressed due to low confidence (1)

docs/file_formatting.md:1

• Corrected spelling of 'potenitally' to 'potentially'.

# File formats of inputs

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[Copilot]

Pull Request Overview

Copilot reviewed 3 out of 5 changed files in this pull request and generated 1 comment.

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