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Pipeline Overview

Note

The DAG below reflects actual process names from main.nf.

flowchart LR
    I[Input multi-FASTA] --> S[SPLIT_FASTA]
    S --> C[CODON_ANALYSIS]
    S --> L[LONG_ORF]
    S --> T[TRANSLATE_FASTA]
    T --> H[HYDROPATHY_PROFILE]
    H --> P[PLOT_HYDROPATHY]
    C --> G[GATHER_RESULTS]
    L --> G
    T --> G
    H --> G
    P --> G

What each stage does

  • SPLIT_FASTA: splits multi-FASTA into single-record FASTA files.
  • CODON_ANALYSIS: runs scripts/codon.pl per record.
  • LONG_ORF: runs scripts/longORF.pl per record.
  • TRANSLATE_FASTA: runs scripts/translate.pl per record.
  • HYDROPATHY_PROFILE: runs scripts/hydropathy.pl per record.
  • PLOT_HYDROPATHY: runs scripts/plot_hydro.py per record.
  • GATHER_RESULTS: merges all per-record outputs into final files.

Tip

Intermediate files are published under ${params.outdir}/intermediate/ for auditability.