Added custom models as submodule, added pipleline for trap species handling (up to alignment). Initial progress on custom model rules

workflow/Snakefile

@@ -15,6 +15,9 @@ module baseline:
     snakefile: "rules/baseline_pipeline.smk"
     config: config
 
+module ml:
+    snakefile: 'rules/ml_pipeline.smk'
+    config: config
 # Pulldown
 rule all:
     input:
@@ -26,8 +29,11 @@ rule all:
         #'../data/pod5_files_to_pull',
         #'../data/basecalled_reads/hac.fastq.gz'
         #expand('../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.pod5',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"]))
-        '../data/aligned_reads/{model}_to_genome.sorted.bam'
+        '../data/aligned_reads/nomiss_hac_to_genome.sorted.bam',
+        '../data/aligned_reads/trap_hac_to_genome.sorted.bam'
+        #'../data/ml_inputs/hac_label_store.pq'
+        #'../data/ml_inputs/model_layouts/cnn_512_4_100000_11_4.json'
 
 use rule * from preparation
 use rule * from baseline
-
+use rule * from ml