move env, config, annot export into the result folder to be self-cont…

…ained
epigen · Sep 13, 2024 · 8f5f44d · 8f5f44d
1 parent dedeb14
commit 8f5f44d
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -99,9 +99,9 @@ rule all:
         expand(os.path.join(result_path,'{group}','{tool}','{db}','{group}_{db}_summary.png'),group=regions["group"].unique(), tool='pycisTarget', db=pycistarget_db_dict.keys()),
         expand(os.path.join(result_path,'{group}','{tool}','{db}','{group}_{db}_summary.png'),group=list(set(genes["group"].tolist()+regions["group"].tolist())), tool='RcisTarget', db=rcistarget_db_dict.keys()),
         # config
-        envs = expand(os.path.join(config["result_path"],'envs',module_name,'{env}.yaml'),env=['region_enrichment_analysis','gene_enrichment_analysis','visualization','pycisTarget','RcisTarget']),
-        configs = os.path.join(config["result_path"],'configs',module_name,'{}_config.yaml'.format(config["project_name"])),
-        annotations = os.path.join(config["result_path"],'configs',module_name,'{}_annot.csv'.format(config["project_name"])),
+        envs = expand(os.path.join(result_path,'envs','{env}.yaml'),env=['region_enrichment_analysis','gene_enrichment_analysis','visualization','pycisTarget','RcisTarget']),
+        configs = os.path.join(result_path,'configs','{}_config.yaml'.format(config["project_name"])),
+        annotations = os.path.join(result_path,'configs','{}_annot.csv'.format(config["project_name"])),
     threads: config.get("threads", 1)
     resources:
         mem_mb=config.get("mem", "16000"),

diff --git a/workflow/rules/envs_export.smk b/workflow/rules/envs_export.smk
@@ -1,15 +1,15 @@
 # one rule per used conda environment to document the exact versions and builds of the used software        
 rule env_export:
     output:
-        report(os.path.join(config["result_path"],'envs','enrichment_analysis','{env}.yaml'),
+        report(os.path.join(result_path,'envs','{env}.yaml'),
                       caption="../report/software.rst", 
                       category="Software", 
-                      subcategory="{}_enrichment_analysis".format(config["project_name"])
+                      subcategory="{}_{}".format(config["project_name"], module_name)
                      ),
     conda:
         "../envs/{env}.yaml"
     resources:
-        mem_mb=1000, #config.get("mem", "16000"),
+        mem_mb=1000,
     threads: config.get("threads", 1)
     log:
         os.path.join("logs","rules","env_{env}.log"),
@@ -21,13 +21,13 @@ rule env_export:
 # add configuration files to report        
 rule config_export:
     output:
-        configs = report(os.path.join(config["result_path"],'configs','enrichment_analysis','{}_config.yaml'.format(config["project_name"])), 
+        configs = report(os.path.join(result_path,'configs','{}_config.yaml'.format(config["project_name"])), 
                          caption="../report/configs.rst", 
                          category="Configuration", 
-                         subcategory="{}_enrichment_analysis".format(config["project_name"])
+                         subcategory="{}_{}".format(config["project_name"], module_name)
                         )
     resources:
-        mem_mb=1000, #config.get("mem", "16000"),
+        mem_mb=1000,
     threads: config.get("threads", 1)
     log:
         os.path.join("logs","rules","config_export.log"),
@@ -40,13 +40,13 @@ rule annot_export:
     input:
         config["annotation"],
     output:
-        annot = report(os.path.join(config["result_path"],'configs','enrichment_analysis','{}_annot.csv'.format(config["project_name"])), 
+        annot = report(os.path.join(result_path,'configs','{}_annot.csv'.format(config["project_name"])), 
                          caption="../report/configs.rst", 
                          category="Configuration", 
-                         subcategory="{}_enrichment_analysis".format(config["project_name"])
+                         subcategory="{}_{}".format(config["project_name"], module_name)
                         )
     resources:
-        mem_mb=1000, #config.get("mem", "16000"),
+        mem_mb=1000,
     threads: config.get("threads", 1)
     log:
         os.path.join("logs","rules","annot_export.log"),