add decomposition of HDP with SigProfilerAssignment and minor fixes

[FerriolCalvet]

Main update: extracted signatures decomposition

The main update is to do the decomposition of the mutational signatures extracted by HDP using SigProfilerAssignment.
This results in a much cleaner assignment of mutational signatures to samples. See example below:

SigProfilerAssignment directly:

Results of SigProfilerAssignment decomposition using the signatures extracted by HDP:

Minor fixes

• Remove all mentions to hg19 and mm10 these are not supported anymore
• Remove some duplicated mutation subsets for exonic mutations

[Copilot]

Pull request overview

Adds a post-processing step to decompose HDP-extracted mutational signatures using SigProfilerAssignment, while also simplifying exon-only mutation subsetting and removing deprecated genome references (hg19/mm10).

Changes:

• Run SigProfilerAssignment decompose_fit on HDP-extracted signatures and publish decomposition outputs.
• Centralize exon-consensus mutation subsetting once in DEEPCSA and pass exon-filtered mutations into downstream selection/mutability analyses.
• Remove hg19/mm10 references from docs/configs/scripts and adjust output publishing paths.

Reviewed changes

Copilot reviewed 15 out of 20 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Adds exon-only mutation subsetting and routes exon-filtered mutations into downstream analyses; tweaks result aggregation condition.
subworkflows/local/signatures_hdp/main.nf	Emits HDP signatures reformatted for SigProfilerAssignment decomposition.
subworkflows/local/signatures/main.nf	Runs SigProfilerAssignment cosmic_fit plus new HDP decomposition step.
subworkflows/local/oncodrive3d/main.nf	Removes redundant mutation/bed intersection; expects pre-filtered mutations.
subworkflows/local/omega/main.nf	Removes redundant mutation/bed intersection; expects pre-filtered mutations.
subworkflows/local/mutability/main.nf	Removes redundant mutation/bed intersection; expects pre-filtered mutations.
subworkflows/local/dnds/main.nf	Removes redundant mutation/bed intersection; expects pre-filtered mutations.
subworkflows/local/adjmutdensity/main.nf	Comment clarification for mutation intersection.
modules/local/signatures/sigprofiler/assignment/decompose_fit/main.nf	New SigProfilerAssignment decompose_fit process for HDP decomposition.
modules/local/signatures/sigprofiler/assignment/cosmic_fit/main.nf	Renames process and updates CLI args for SigProfilerAssignment 1.1.3.
modules/local/signatures/hdp/reformat_sigs/main.nf	New process to reformat HDP signatures into SigProfilerAssignment-compatible TSV.
modules/local/signatures/hdp/process_results/main.nf	Exposes extracted signature components file as a workflow output.
conf/modules.config	Updates publish paths and adds publish rules for new decomposition/reformat steps; removes deprecated genome mappings.
conf/tools/omega.config	Removes deprecated genome mappings.
docs/usage.md	Updates supported genome note (GRCh38 only) for external resources.
bin/utils_context.py	Removes deprecated genome imports.
bin/sites_table_from_positions.py	Removes hg19/mm10 options and mapping.
bin/postprocessing_annotation.py	Removes hg19/mm10 options and mapping.
bin/panel_postprocessing_annotation.py	Removes hg19/mm10 options and mapping.
subworkflows/local/oncodriveclustl/main.nf	Minor formatting/alignment change.

Comments suppressed due to low confidence (2)

workflows/deepcsa.nf:405

• DNDS subworkflow no longer takes a bedfile input (see subworkflows/local/dnds/main.nf), but this call still passes CREATEPANELS.out.exons_consensus_bed as a third argument. This will cause a Nextflow compilation/runtime error due to mismatched inputs. Update the call to pass only the inputs expected by DNDS (mutations, depth, panel) or reintroduce the bedfile input consistently.

        DNDS(mutations_in_exons,
                    DEPTHSEXONSCONS.out.subset,
                    CREATEPANELS.out.exons_consensus_bed,
                    CREATEPANELS.out.exons_consensus_panel
                    )

modules/local/signatures/sigprofiler/assignment/cosmic_fit/main.nf:56

• The stub: section only creates a PDF, but the process declares TXT outputs (stats and mutation_probs). In stub mode this will fail due to missing expected outputs. Update the stub to create placeholder TXT files that match the declared glob patterns (and keep versions.yml).

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