Processes

SPLIT_FASTA

Note

Input: params.input multi-FASTA.

flowchart LR
    A[params.input] --> B[SPLIT_FASTA]
    B --> C[*.fa per record]

CODON_ANALYSIS (scripts/codon.pl)

Warning

This process computes many metrics, including codon-level and entropy statistics.

flowchart LR
    A[record.fa] --> B[CODON_ANALYSIS]
    B --> C[id.metrics.txt]

LONG_ORF (scripts/longORF.pl)

flowchart LR
    A[record.fa] --> B[LONG_ORF]
    B --> C[id.orf]
    B --> D[id.orf.fasta]

TRANSLATE_FASTA (scripts/translate.pl)

flowchart LR
    A[record.fa] --> B[TRANSLATE_FASTA]
    B --> C[id.translated.fasta]

HYDROPATHY_PROFILE (scripts/hydropathy.pl)

flowchart LR
    A[id.translated.fasta] --> B[HYDROPATHY_PROFILE]
    B --> C[id.hplot.txt]
    B --> D[id.hsummary.txt]

PLOT_HYDROPATHY (scripts/plot_hydro.py)

flowchart LR
    A[id.hplot.txt] --> B[PLOT_HYDROPATHY]
    B --> C[id.hplot.png]

HEATMAP_PLOT (scripts/heatmap.sh)

Generates a 2-D genome hydropathy heatmap by binning the per-position hydropathy values from HYDROPATHY_PROFILE into a symmetric matrix and rendering it with gnuplot.

Input: id.hplot.txt produced by HYDROPATHY_PROFILE. Output: one PNG file named <prefix>_<id>.png (a diverging Blue–White–Red heatmap of average hydropathy across genomic windows).

flowchart LR
    A[id.hplot.txt] --> B[HEATMAP_PLOT]
    B --> C[id_seqname.png]

CODON_PLOTS (scripts/codon_plots.py)

Produces a multi-panel figure visualising codon usage metrics from CODON_ANALYSIS: nucleotide composition pie chart, scalar sequence metrics, ORF statistics, codon-count heatmap, RSCU heatmap, amino-acid composition bar chart, and sliding-window GC%.

Input: id.metrics.txt produced by CODON_ANALYSIS. Output: id.codon_plots.png and id.codon_plots.pdf.

flowchart LR
    A[id.metrics.txt] --> B[CODON_PLOTS]
    B --> C[id.codon_plots.png]
    B --> D[id.codon_plots.pdf]

GATHER_RESULTS

Danger

This is the terminal merge stage and rewrites combined outputs under ${params.outdir}/codonanalyzer_results/.

flowchart LR
    A[metrics/orf/translated/hplot/hsummary/png] --> B[GATHER_RESULTS]
    B --> C[metrics.txt]
    B --> D[orf + orf.fasta]
    B --> E[translated.fasta]
    B --> F[hplot.txt + hsummary.txt]
    B --> G[hplot PNGs]