Expand deepCSA documentation coverage and output interpretation

[Copilot]

The issue called for a comprehensive documentation pass: clarify deepUMIcaller inputs, data sources, output interpretation, examples, and citation coverage while documenting toggles and QC guidance. This update focuses on filling the missing pipeline documentation gaps across usage, file formats, output interpretation, tools, and citations.

• Inputs & data sources
  • DeepUMIcaller VCF/BAM selection guidance, batch/sample handling
  • Explicit download sources for VEP, CADD, dNdScv, Oncodrive3D, GFF3
  • NanoSeq mask usage and parameters
• Outputs & interpretation
  • Output directory cheat sheet and PMEAN/PSTD behavior
  • QC/sanity checks, omega vs omegagloballoc, site selection metrics
  • Signature outputs and profile stability interpretation
• Examples & formats
  • Blacklist, gene grouping, subgenic/hotspot region examples
  • Expanded file-format descriptions (CADD, dNdScv, WGS trinuc counts)
• Tooling & provenance
  • Container image list with override guidance
  • CITATIONS expanded to cover intermediate tools and repositories

Example config snippet (from docs) showing new guidance:

params {
    nanoseq_snp   = "SNP_GRCh38.wgns.bed.gz"
    nanoseq_noise = "NOISE_GRCh38.wgns.bed.gz"
    plot_only_allsamples = true
    positive_selection_non_protein_affecting = true
}

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• www.protocols.io
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)