snakefmt

Author: gibsramen

workflow/rules/common.smk

@@ -28,7 +28,7 @@ all_viz_files.extend(
     expand(
         "figures/{curve}/{curve}.pctile_{pctile}.svg",
         pctile=config["log_ratio_feat_pcts"],
-        curve=["pr", "roc"]
+        curve=["pr", "roc"],
     )
 )
 all_viz_files.append("figures/rank_comparisons.html")
@@ -56,5 +56,5 @@ diffab_tool_columns = {
     "songbird": f"C({covariate}, Treatment('{reference}'))[T.{target}]",
     "maaslin2": "coef",
     "metagenomeseq": f"{covariate}{target}",
-    "corncob": "coefs"
+    "corncob": "coefs",
 }

workflow/rules/visualization.smk

@@ -31,7 +31,7 @@ rule plot_rank_correlation:
             "figures/spearman_heatmap.svg",
             caption="../report/plot_rank_correlation.rst",
             category="Differentials",
-            subcategory="Comparison"
+            subcategory="Comparison",
         ),
     log:
         "log/plot_rank_correlation.log",
@@ -124,7 +124,7 @@ rule plot_pca:
             "figures/pca.svg",
             caption="../report/plot_pca.rst",
             category="Differentials",
-            subcategory="Comparison"
+            subcategory="Comparison",
         ),
     log:
         "log/plot_pca.log",
@@ -142,7 +142,7 @@ rule plot_rank_comparison:
             "figures/rank_comparisons.html",
             caption="../report/plot_rank_comparison.rst",
             category="Differentials",
-            subcategory="Comparison"
+            subcategory="Comparison",
         ),
     log:
         "log/plot_rank_comparison.log",
@@ -163,7 +163,7 @@ rule qurro:
             caption="../report/qurro.rst",
             htmlindex="index.html",
             category="Differentials",
-            subcategory="Comparison"
+            subcategory="Comparison",
         ),
     log:
         "log/qurro.log",
@@ -187,7 +187,7 @@ rule create_table:
             "results/differentials_table.html",
             caption="../report/create_table.rst",
             category="Differentials",
-            subcategory="Comparison"
+            subcategory="Comparison",
         ),
     log:
         "log/create_table.log",