Add HEATMAP_PLOT and CODON_PLOTS processes to Nextflow pipeline

[Copilot]

Integrates two previously isolated scripts (heatmap.sh, codon_plots.py) as first-class Nextflow processes, wired into the existing channel flow and gathered into final results.

New processes

• HEATMAP_PLOT — consumes HYDROPATHY_PROFILE.out.hplot (.hplot.txt), runs heatmap.sh to produce a gnuplot diverging-palette PNG heatmap; output glob *.png since the filename embeds the sequence name extracted from the data file at runtime
• CODON_PLOTS — consumes CODON_ANALYSIS.out.metrics (.metrics.txt), runs codon_plots.py to produce a 7-panel codon usage figure as both .png and .pdf

Pipeline wiring

HEATMAP_PLOT(HYDROPATHY_PROFILE.out.hplot)
CODON_PLOTS(CODON_ANALYSIS.out.metrics)

GATHER_RESULTS extended with three new positional inputs (heatmap_pngs, codon_plot_pngs, codon_plot_pdfs), each collected via the same toSortedList/map pattern used by all existing channels. The heatmap_png channel additionally calls .flatten() since each process invocation may emit multiple files.

Docs

Added HEATMAP_PLOT and CODON_PLOTS sections to docs/processes.md matching the existing heading level, admonition style, and Mermaid diagram format.