strainify

#!/usr/bin/env bash
set -euo pipefail

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
SNAKEFILE="$SCRIPT_DIR/Snakefile"
FILTER_SCRIPT="$SCRIPT_DIR/filter_genomes.sh"

usage() {
    cat <<EOF
Strainify CLI

Usage:
  strainify run [snakemake args...]
  strainify filter-run [filter args...]

Commands:
  run
      Run Snakemake pipeline directly

      Example:
        strainify run --cores 12 --configfile config.yaml

  filter-run
      Run genome filtering + pipeline

      Example:
        strainify filter-run \\
          --genomes genomes \\
          --fastqs fastqs \\
          --out results \\
          --config config.yaml \\
          --threads 12

  help
      Show this message
EOF
    exit 1
}

# ----------------------------
# Parse command
# ----------------------------
if [[ $# -lt 1 ]]; then
    usage
fi

CMD="$1"
shift

case "$CMD" in
    run)
        if [[ ! -f "$SNAKEFILE" ]]; then
            echo "ERROR: Snakefile not found at $SNAKEFILE" >&2
            exit 1
        fi

        snakemake --snakefile "$SNAKEFILE" "$@"
        ;;

    filter-run)
        if [[ ! -f "$FILTER_SCRIPT" ]]; then
            echo "ERROR: filter script not found: $FILTER_SCRIPT" >&2
            exit 1
        fi

        # auto-fix permissions if needed
        if [[ ! -x "$FILTER_SCRIPT" ]]; then
            chmod +x "$FILTER_SCRIPT" || {
                echo "ERROR: Could not make filter script executable" >&2
                exit 1
            }
        fi

        "$FILTER_SCRIPT" "$@"
        ;;

    help|-h|--help)
        usage
        ;;

    *)
        echo "ERROR: Unknown command: $CMD" >&2
        usage
        ;;
esac