added a bam path function for a CONCOT parameter

magneto/rules/binning.smk

@@ -398,6 +398,14 @@ def concoct_bam_input(wildcards):
                     ), src=assembly_dict.get(assembly_request))
     return inputs
 
+def path_to_bam(wildcards):
+    if "CASB" in strategies or "CACB" in strategies:
+        path = os.path.join(intermediate_results_dir, "assembly/co_assembly/megahit/" + wildcards.src + "/compute_depth/*.sorted.bam")
+        return path
+    if "SASB" in strategies or "SACB" in strategies:
+        path = os.path.join(intermediate_results_dir, "assembly/single_assembly/megahit/" + wildcards.src + "/compute_depth/*.sorted.bam")
+        return path
+
 rule concoct_coverage_table:
     '''
         Generate table with coverage depth information per sample and subcontig
@@ -411,7 +419,7 @@ rule concoct_coverage_table:
         os.path.join(CONDAENV, "concoct.yaml")
     threads: 5
     params:
-        bam_path = os.path.join(intermediate_results_dir, "assembly/single_assembly/megahit/{src}/compute_depth/*.sorted.bam"),
+        bam_path = path_to_bam
     shell:
         "concoct_coverage_table.py {input[0]} {params.bam_path} > {output.coverage} "