intial version

workflow/scripts/download_reference_sequences.py

@@ -0,0 +1,11 @@
+from typing import TYPE_CHECKING
+from pathlib import Path
+if TYPE_CHECKING:
+    from snakemake.iocontainers import snakemake
+
+
+
+def download_species_fasta(species_name:str, ncbi_datasets_binary: str, tmp_dir : Path) -> Path:
+    """Download the reference genome fasta for a given species"""
+    output_fasta = tmp_dir / f'{species_name}.fasta'
+