intial version

workflow/Snakefile

@@ -0,0 +1,32 @@
+import os
+from dotenv import load_dotenv
+
+load_dotenv()
+
+configfile: "config/main.yaml"
+configfile: "config/dependencies.yaml"
+configfile: "../reference/species_list.yaml"
+
+module preparation:
+    snakefile: "rules/preparation.smk"
+    config: config
+
+module baseline:
+    snakefile: "rules/baseline_pipeline.smk"
+    config: config
+
+# Pulldown
+rule all:
+    input:
+        #"binaries/datasets",
+        #f"{config['dorado_model_dir']}/{config['fast_model_name']}",
+        #f"{config['dorado_model_dir']}/{config['hac_model_name']}",
+        #'../data/reference_genomes/full_reference.mmi',
+        #'../data/raw_pod5/'
+        #'../data/pod5_files_to_pull',
+        #'../data/basecalled_reads/hac.fastq.gz'
+        expand('../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.fastq.gz',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"]))
+
+use rule * from preparation
+use rule * from baseline
+