miscellaneous updates

[FerriolCalvet]

Updates

• allow new input format! users can provide a MAF file as input for deepCSA
• update plots to use proper colors for SBS mutations
• generate mutation matrix for running MSA
• enable cache of all steps (we will have to assess the impact in terms of cache size
• add jupyter notebooks to customly downsample samples to a desired depth

Mandatory tasks

• Document the new input format and all new parameters
• Ensure proper definition of mandatory and optional parameters

[FerriolCalvet]

looks good!

[Copilot]

Pull request overview

This PR updates the deepCSA Nextflow pipeline to support alternate mutation inputs and additional downstream outputs, while also adjusting plotting and depth/panel utilities.

Changes:

• Add support for providing mutations via a MAF file (converted to per-sample VCFs) in the main workflow.
• Extend signature-matrix generation to additionally produce MSA-formatted mutation matrices.
• Adjust plotting/color handling and make depth/panel utilities robust to presence/absence of a CONTEXT column; enable caching more broadly.

Reviewed changes

Copilot reviewed 13 out of 20 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Adds input_maf handling path (MAF→VCF) and wires it into downstream steps
subworkflows/local/enrichpanels/main.nf	Removes unused bedfile inputs from ENRICHPANELS interface
nextflow_schema.json	Adds input_maf parameter; removes create_sample_panels
nextflow.config	Adds params.input_maf default
modules/nf-core/tabix/bgziptabixquery/main.nf	Enables caching by removing explicit cache false
modules/nf-core/tabix/bgziptabix/main.nf	Enables caching by removing explicit cache false
modules/local/sig_matrix_concat/main.nf	Emits new *.msa.csv matrix outputs
modules/local/downsample/mutations/main.nf	Enables caching by removing explicit cache false (non-deterministic step)
modules/local/analyzedepths/main.nf	Tweaks inputs/formatting and adds versions output
conf/test_real.config	Adds commented example params for MAF/custom-depth mode
conf/modules.config	Adds config block for INPUTMAF2VCF publishing/args
conf/general_files_IRB.config	Formatting/alignment changes
bin/utils_plot.py	Adds color mapping for - mutation type
bin/plot_maf.py	Uses custom SBS colors for MUTTYPE plots; refactors plotting into multi-figure returns
bin/merge_annotation_depths.py	Drops CONTEXT column if present before joining
bin/deepcsa_maf2samplevcfs.py	Adds support for AM depth columns and new FORMAT fields
bin/create_consensus_panel.py	Drops CONTEXT column if present before numeric casts
bin/concat_sigprot_matrices.py	Refactors matrix saving and adds MSA matrix generation
assets/useful_scripts/downsample_depths.ipynb	Removed notebook
assets/useful_scripts/downsample.ipynb	Adds notebook for custom downsampling workflow

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[FerriolCalvet]

@copilot fix the comments provided ensuring that the pipeline can be executed properly
provide documentation on the alternative input modes that will be enabled by merging this PR

[Copilot]

@FerriolCalvet I've opened a new pull request, #432, to work on those changes. Once the pull request is ready, I'll request review from you.

[FerriolCalvet]

all good!