Accept methods outputs and genome config file.

Data_submission/build_file_dicts.py

@@ -229,10 +229,14 @@ def main():
             assert not common_vars, f"Variable overwriting hazard!\n{common_vars}"
             vars_from_analyses |= set(analysis_config.keys())
             # This may be needed for analysis types with configurable genome
-            genome = analysis_config.get(
+            genome_dict = analysis_config.get(
                 "genome_dict",
                 # default genome name will be "C_elegans"
-                {"name": "C_elegans"})["name"]
+                {"name": "C_elegans"})
+            if isinstance(genome_dict, (str, bytes)):
+                with open(analysis_config["genome_dict"]) as gendict_fh:
+                    genome_dict = yload(gendict_fh)
+            genome = genome_dict["name"]
             # Load the snakefile to get information
             # about the rule making bigwig files
             # Based on snakemake/__init__.py and snakemake/workflow.py
@@ -253,7 +257,16 @@ def main():
             #after_loading_vars = list(recdir())
             # Use pattern matching so that it fails if we have not exactly
             # one bigwig file in the output of the rule
+            try:
                 [bw_pattern] = sf._rules[bw_rulename].output
+            except ValueError:
+                try:
+                    # Sometimes, a rule may also output a "methods" file
+                    [bw_pattern, methods_pattern] = sf._rules[bw_rulename].output
+                    assert methods_pattern.endswith("_methods.txt")
+                except ValueError:
+                    print(analysis_snakefile, bw_rulename, file=sys.stderr)
+                    raise
             #for varname in set(after_loading_vars) - set(before_loading_vars):
             #    # https://stackoverflow.com/a/26545111/1878788
             #    del globals()[varname]