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metagenome-atlas · Jul 29, 2024 · d851220 · d851220
1 parent 11f6b6f
commit d851220
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/atlas/make_config.py b/atlas/make_config.py
@@ -21,9 +21,9 @@ def make_default_config():
 
     config["simplejob_mem"] = 10
     config["simplejob_threads"] = 4
-    config[
-        "importqc_params"
-    ] = "iupacToN=t touppercase=t qout=33 addslash=t trimreaddescription=t"
+    config["importqc_params"] = (
+        "iupacToN=t touppercase=t qout=33 addslash=t trimreaddescription=t"
+    )
 
     config["mem"] = MEM
     config["large_mem"] = 250

diff --git a/workflow/report/bin_report.py b/workflow/report/bin_report.py
@@ -68,9 +68,9 @@ def add_stats(name, d):
     add_stats("All", df)
 
     df.eval("Quality_score = Completeness - 5* Contamination", inplace=True)
-    div[
-        "QualityScore"
-    ] = "<p>Quality score is calculated as: Completeness - 5 x Contamination.</p>"
+    div["QualityScore"] = (
+        "<p>Quality score is calculated as: Completeness - 5 x Contamination.</p>"
+    )
     add_stats("Quality score >50 ", df.query("Quality_score>50"))
     add_stats("Good quality", df.query("Completeness>90 & Contamination <5"))
     add_stats("Quality score >90 ", df.query("Quality_score>90"))

diff --git a/workflow/report/qc_report.py b/workflow/report/qc_report.py
@@ -236,9 +236,9 @@ def make_plots(
 
     ### Insert insert_size_stats
     if insert_size_stats is None:
-        div[
-            "Insert"
-        ] = "<p>Insert size information is not available for single end reads.</p>"
+        div["Insert"] = (
+            "<p>Insert size information is not available for single end reads.</p>"
+        )
     else:
         data_insert = pd.read_table(insert_size_stats, index_col=0)
         data_insert.index.name = "Sample"