{
  "name": "phylogeny-flow",
  "version": "0.1.0-r1",
  "started_at": "2026-05-28T17:32:41Z",
  "completed_at": "2026-05-28T17:32:53Z",
  "outdir": "cytc-out",
  "input": "tests/fixtures/cytochrome-c-uniprot-reviewed-v1/sequences/cytochrome_c_24.fa",
  "parameters": {
    "input_mode": "raw_fasta",
    "seq_type": "protein",
    "aligner": "mafft",
    "trimmer": "trimal",
    "tree_engine": "iqtree",
    "model": "LG",
    "bootstrap": "0",
    "alrt": "0",
    "threads": "6",
    "seed": "20260528",
    "plot_tree": "true",
    "plot_layout": "rectangular",
    "plot_formats": "pdf,png,svg",
    "plot_style": "journal",
    "plot_gallery_layouts": "rectangular,circular",
    "plot_label_align": "none",
    "plot_label_transform": "pretty",
    "plot_scale_bar": "auto"
  },
  "outputs": {
    "tree": "03_results/tree/tree.nwk",
    "alignment": "03_results/alignment/aligned.fa",
    "trimmed_alignment": "03_results/alignment/trimmed.fa",
    "tree_plot_status": "generated",
    "tree_plot_dir": "03_results/tree/plots",
    "tree_plot_gallery": "03_results/tree/plots/tree_plot_gallery.tsv",
    "report": "04_reports/phylogeny_report.html"
  }
}