2.2.2: fixes and small update

weber8thomas · Sep 22, 2023 · 38150e5 · 38150e5
1 parent 9f2f2fa
commit 38150e5
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Showing 3 changed files with 25 additions and 15 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -1,9 +1,6 @@
-from snakemake.utils import min_version
-
-# min_version("7.14.0")
+configfile_location = "config/config.yaml"
 
 
-configfile_location = "config/config.yaml"
 configfile: configfile_location
 
 

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -63,9 +63,13 @@ if config["mosaicatcher_pipeline"] == False:
         )
 
 
-def onsuccess_fct(log): 
-    config_metadata = config_definitions = yaml.safe_load(open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r"))
-    log_path_new = make_log_useful_ashleys.make_log_useful(log, "SUCCESS", config, config_metadata)
+def onsuccess_fct(log):
+    config_metadata = config_definitions = yaml.safe_load(
+        open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r")
+    )
+    log_path_new = make_log_useful_ashleys.make_log_useful(
+        log, "SUCCESS", config, config_metadata
+    )
     shell(
         'mail -s "[Snakemake] smk-wf-catalog/ashleys-qc-pipeline v{} - Run on {} - SUCCESS" {} < {}'.format(
             config["version"], config["data_location"], config["email"], log_path_new
@@ -74,14 +78,19 @@ def onsuccess_fct(log):
 
 
 def onerror_fct(log):
-    config_metadata = config_definitions = yaml.safe_load(open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r"))
-    log_path_new = make_log_useful_ashleys.make_log_useful(log, "ERROR", config, config_metadata)
+    config_metadata = config_definitions = yaml.safe_load(
+        open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r")
+    )
+    log_path_new = make_log_useful_ashleys.make_log_useful(
+        log, "ERROR", config, config_metadata
+    )
     shell(
         'mail -s "[Snakemake] smk-wf-catalog/ashleys-qc-pipeline v{} - Run on {} - ERRROR" {} < {}'.format(
             config["version"], config["data_location"], config["email"], log_path_new
         )
     )
 
+
 # Simple class to retrieve automatically files in the fastq/bam folder and create a config dataframe
 class HandleInput:
     def __init__(
@@ -264,7 +273,11 @@ class HandleInput:
             "strandphaser",
         ]
 
-        for sample in [e for e in os.listdir(thisdir) if e not in exclude and e.endswith(".zip") is False]:
+        for sample in [
+            e
+            for e in os.listdir(thisdir)
+            if e not in exclude and e.endswith(".zip") is False
+        ]:
             # Create a list of  files to process for each sample
             l_files_all = [
                 f

diff --git a/workflow/rules/count.smk b/workflow/rules/count.smk
@@ -112,11 +112,11 @@ rule plot_mosaic_counts:
     output:
         # "{folder}/{sample}/plots/counts/CountComplete.raw.pdf",
         report(
-                "{folder}/{sample}/plots/counts/CountComplete.raw.pdf",
-                category="Mosaic Counts",
-                subcategory="{sample}",
-                labels={"Cell": "ALL", "Type": "raw"},
-            ),
+            "{folder}/{sample}/plots/counts/CountComplete.raw.pdf",
+            category="Mosaic Counts",
+            subcategory="{sample}",
+            labels={"Cell": "ALL", "Type": "raw"},
+        ),
     log:
         "{folder}/log/plot_mosaic_counts/{sample}.log",
     params: