Add depth-vs-metric QC plots and summaries for mutdensity/omega outputs

[Copilot]

This PR adds QC focused on how sequencing depth relates to mutagenesis/selection metrics, using compiled cohort outputs and per-gene per-sample depth tables. It introduces scatterplot outputs (per sample) and TSV summaries to quantify depth effects and highlight depth-associated missingness.

• New QC capability: metric vs depth (per sample, per gene points)

  • Added bin/metrics_vs_depth_qc.py to analyze:
    • all_mutdensities.tsv (required)
    • all_adjusted_mutdensities.tsv (optional)
    • all_omegas*_global_loc.tsv (optional)
    • all_groups.json + *.depth_per_gene_per_sample.tsv
  • Generates:
    • paginated scatterplot PDFs (metric vs MEAN_GENE_DEPTH, split by sample)
    • depth-effect summaries (pearson/spearman, slope, p-value)
    • missingness summaries per gene (fraction missing + depth context)

• Pipeline integration

  • Added module: modules/local/plot/qc/metrics_vs_depth/main.nf (PLOT_METRICS_VS_DEPTH_QC)
  • Wired into QC subworkflow: subworkflows/local/plotting_qc/main.nf
  • Wired required/optional inputs in main workflow: workflows/deepcsa.nf
  • Optional inputs are handled so mutdensity-depth QC still runs when omega global-loc is unavailable.

• Published outputs and docs

  • Added publish route for the new process:
    • qc/metrics_vs_depth in conf/results_outputs.config
  • Updated output docs (docs/output.md) to include the new QC artifact group.
  • Added minimal placeholder asset for optional-channel fallback (assets/placeholder_no_file.tsv).

• Test surface update

  • Updated tests/deepcsa.nf.test omega scenario to assert presence of the new QC output directory.

PLOTMETRICSVSDEPTHQC(
    all_mutdensities,
    average_depth_gene_sample.map { it[1] },
    groups_definition,
    group_name,
    all_adjusted_mutdensities,
    all_omegas_globalloc
)

[FerriolCalvet]

tested and it works!

[Copilot]

Pull request overview

Adds a new QC analysis to relate sequencing depth to mutagenesis/selection metrics, wiring it into the DeepCSA plotting QC path and publishing the resulting plots/tables.

Changes:

• Introduces bin/metrics_vs_depth_qc.py and a new Nextflow process PLOT_METRICS_VS_DEPTH_QC to generate metric-vs-depth PDFs and TSV summaries.
• Integrates the new QC step into the QC plotting subworkflow and main workflow wiring, including placeholder handling for optional inputs.
• Adds a publishDir route and documents the new output location.

Reviewed changes

Copilot reviewed 8 out of 9 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Wires new QC inputs into PLOTTINGQC and adds placeholder channels for optional inputs.
subworkflows/local/plotting_qc/main.nf	Includes and invokes the new metrics-vs-depth QC module; emits new outputs.
modules/local/plot/qc/metrics_vs_depth/main.nf	New Nextflow process wrapper around metrics_vs_depth_qc.py with stub outputs.
bin/metrics_vs_depth_qc.py	New QC implementation producing scatterplot PDFs and depth-effect/missingness TSV summaries.
conf/results_outputs.config	Publishes outputs under qc/metrics_vs_depth.
conf/modules.config	Adds process config for optional-arg gating via task.ext.*.
docs/output.md	Documents the new QC output path.
assets/placeholder_no_file.tsv	Placeholder file used for optional-channel fallbacks.
tests/deepcsa.nf.test	Minor edit (removes trailing blank line).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.