New release: v1.0.0 Ter

[FerriolCalvet]

• add plotting selection, saturation, qc
• add tests init
• update some input definitions, with new parameters
• add Nanoseq masks

[Copilot]

Pull Request Overview

This PR prepares the v1.0.0 release by adding plotting summaries/QC, signature matrix generation, NanoSeq masks, parameter schema updates, and initial nf-test coverage.

• Add cohort/group plotting subworkflows (summary, saturation, inter-individual variability) and QC plots for mutation densities and omega global/local sanity checks
• Introduce NanoSeq SNP/noise masks and new input/config parameters; rework several modules’ CLIs and containers to 0.0.2-alpha
• Add initial nf-test tests and config; wire new adjusted mutational density and signatures (MAF→VCF → SigProfiler MatrixGenerator)

Reviewed Changes

Copilot reviewed 117 out of 156 changed files in this pull request and generated 21 comments.

Show a summary per file

File	Description
workflows/tests/deepcsa.nf.test	Adds first pipeline-level nf-test (minimal run)
workflows/deepcsa.nf	Wires new subworkflows (plotting summary/QC), adjusted mutdensity, signatures VCF/matrix, and NanoSeq integration
tests/nextflow.config	Test profile/config for nf-test (params, singularity, executor)
test_data/modules/PPM1D_exons.bed4.bed	Test fixtures for EXPAND_REGIONS
test_data/modules/PPM1D_domains.bed4.bed	Test fixtures for EXPAND_REGIONS
subworkflows/local/signatures_hdp/main.nf	Hdp extraction subworkflow cleanup
subworkflows/local/signatures/main.nf	Integration of HDP extraction path
subworkflows/local/plottingsummary/main.nf	New summary plotting subworkflow (selection, saturation, variability)
subworkflows/local/plotting_qc/main.nf	New QC plotting subworkflow (mutdensity QC)
subworkflows/local/omega/main.nf	Adds global/local omega evaluation, site comparison wiring, and all-results collection
subworkflows/local/mutationpreprocessing/main.nf	Adds NanoSeq masks, contamination check, grouped output, and improved plotting selection
subworkflows/local/mutatedcells/vaf/main.nf	Clean up conditional
subworkflows/local/dnds/main.nf	Moves covariates/refs loading inside subworkflow
subworkflows/local/createpanels/main.nf	Domain annotation input now comes from params.domains_file; emits domains info TSV
subworkflows/local/adjmutdensity/main.nf	New adjusted mutational density subworkflow
nf-test.config	nf-test harness configuration
nextflow_schema.json	Adds/renames parameters (groups, domains_file, omega_subgenic_bedfile, plot_only_allsamples, NanoSeq masks, gnomad_af_threshold, etc.)
nextflow.config	Defaults for new params, profiles refactor, tmp quick fixes include
modules/local/writemaf/main.nf	Bump core container to 0.0.2-alpha
modules/local/vcf2maf/main.nf	Switch to new CLI (args)
modules/local/table2groups/main.nf	New CLI options (unique identifier, groups list); container bump
modules/local/subsetmaf/main.nf	Optional output; min_mutations support
modules/local/sitesfrompositions/main.nf	Container bump
modules/local/signatures/sigprofiler/matrixgenerator/main.nf	New module for SigProfiler MatrixGenerator
modules/local/signatures/sigprofiler/extractor/main.nf	Not in use (documented); placeholder
modules/local/signatures/musical/main.nf	Not in use (documented); placeholder
modules/local/signatures/msighdp/main.nf	Not in use (documented); minor cleanups
modules/local/signatures/hdp/process_results/main.nf	Switch container to hdp_wrapper
modules/local/signatures/hdp/prepareinput/main.nf	Switch container to hdp_wrapper
modules/local/signatures/hdp/normalize_sigs/main.nf	Switch container to hdp_wrapper
modules/local/signatures/hdp/compare_sigs/main.nf	Switch container to hdp_wrapper
modules/local/sig_matrix_concat/main.nf	Container bump
modules/local/select_mutdensity/main.nf	Container bump
modules/local/runregressions/main.nf	Container bump
modules/local/process_annotation/panelcustom/main.nf	Container bump
modules/local/process_annotation/panel/main.nf	Container bump
modules/local/process_annotation/mutations_custom/main.nf	Container bump
modules/local/process_annotation/mutations/main.nf	Update CLI to add gnomAD threshold and flags; container bump
modules/local/process_annotation/domain/main.nf	Emit domains TSV; container bump
modules/local/plot/selection_metrics/main.nf	Update CLI usage/outdir; container bump
modules/local/plot/saturation/main.nf	New saturation plot process
modules/local/plot/qc/mutation_densities/main.nf	New mutdensity QC plot process
modules/local/plot/qc/globalloc_synonymous/main.nf	New omega syn QC plot process
modules/local/plot/omega/main.nf	Update CLI/outdir; container bump
modules/local/plot/needles/main.nf	Update CLI/outdir; container bump
modules/local/plot/mutations_summary/main.nf	Update CLI and JSON filters; container bump
modules/local/plot/interindividual_variability/main.nf	New variability plot process
modules/local/plot/depths_summary/main.nf	Container bump
modules/local/mutations2sbs/main.nf	Container bump
modules/local/mutation_matrix/main.nf	Container bump
modules/local/mutated_genomes_from_vaf/main.nf	Optional output; container bump
modules/local/mut_density/main.nf	New module to compute adjusted mut density
modules/local/mergemafs/main.nf	Container bump
modules/local/maf2vcf/main.nf	New MAF→VCF module
modules/local/indels/main.nf	Container bump
modules/local/group_genes/main.nf	Container bump
modules/local/filtermaf/main.nf	Container bump
modules/local/filterbed/main.nf	New CLI with positive filter support; container bump
modules/local/expand_regions/tests/...	Adds nf-test for EXPAND_REGIONS
modules/local/expand_regions/main.nf	Refactor inputs for domains/exons/custom; container bump
modules/local/downsample/mutations/main.nf	Container bump
modules/local/downsample/depths/main.nf	Container bump
modules/local/dnds/preprocess/main.nf	Container bump
modules/local/dna2protein/main.nf	Adds depths input; emits per-exon depths and exon BED; container bump
modules/local/createpanels/consensus/main.nf	Genes subset default fix
modules/local/contamination/main.nf	New contamination check module
modules/local/computemutdensity/main.nf	Container bump
modules/local/compute_trinucleotide/main.nf	Container bump
modules/local/compute_profile/main.nf	Container bump
modules/local/compute_mutability/main.nf	Container bump
modules/local/combine_sbs/main.nf	Container bump
modules/local/blacklistmuts/main.nf	Container bump
modules/local/bbgtools/sitecomparison/main.nf	Container bump
modules/local/bbgtools/oncodrive3d/run/main.nf	Use bbglab/oncodrive3d and version capture; log pattern tweak
modules/local/bbgtools/oncodrive3d/preprocessing/main.nf	Container bump
modules/local/bbgtools/oncodrive3d/plot_chimerax/main.nf	Version capture fix
modules/local/bbgtools/oncodrive3d/plot/main.nf	Use bbglab/oncodrive3d and version capture; log pattern tweak
docs/...	Updates to usage, tools rationale, formats, issues, README
conf/...	Many config/profile updates, new modes, tmp fixes, tool configs, domain file and masks wiring
nf-test.config	Config for nf-test
LICENSE	Replaces placeholder license with AGPL notice
CITATIONS.md	Adds sources/tools references

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

[Copilot]

Pull Request Overview

Copilot reviewed 117 out of 156 changed files in this pull request and generated 9 comments.

Comments suppressed due to low confidence (1)

nextflow_schema.json:592

• Corrected spelling of 'Comma-separeted' to 'Comma-separated'.

                "selected_genes": {
                    "type": "string",
                    "description": "Comma-separeted list of genes to focus the analysis",
                    "fa_icon": "fas fa-book",

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}