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Note

codonanalyzer is a Nextflow DSL2 pipeline that runs codon usage, ORF detection, translation, and hydropathy analysis for each record in a DNA multi-FASTA file.

Tip

For production runs on 96 cores / 1 TB RAM, use the hpc profile and tune conf/resources.config if your SLURM partition has stricter limits.

End-to-end workflow

flowchart LR
    A[params.input multi-FASTA] --> B[SPLIT_FASTA]
    B --> C[CODON_ANALYSIS]
    B --> D[LONG_ORF]
    B --> E[TRANSLATE_FASTA]
    E --> F[HYDROPATHY_PROFILE]
    F --> G[PLOT_HYDROPATHY]
    C --> H[GATHER_RESULTS]
    D --> H
    E --> H
    F --> H
    G --> H
    H --> I[Final outputs in params.outdir]

Warning

Inputs with extremely long records can increase runtime in CODON_ANALYSIS and LONG_ORF because both scripts process complete sequence content.