Merge branch 'fix-hub-supertracks' into fix-refactor-designip

alsmith151 · Apr 22, 2024 · 86978ba · 86978ba
2 parents ef48a19 + 779330d
commit 86978ba
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/seqnado/workflow/rules/hub.smk b/seqnado/workflow/rules/hub.smk
@@ -25,16 +25,16 @@ def get_hub_params(config):
         "subgroup_by": config["ucsc_hub_details"].get(
             "subgroup_by",
             [
-                "pileup_method",
+                "method",
                 "norm"
             ],
         ),
-        "supergroup_by": config["ucsc_hub_details"].get("supergroup_by", None),
+        "supergroup_by": config["ucsc_hub_details"].get("supergroup_by", "ext"),
     }
 
     if ASSAY == "RNA":
-        hub_params["overlay_by"] = ["samplename", "pileup_method", "norm"]
-        hub_params["subgroup_by"] = ["samplename", "pileup_method", "norm", "strand"]
+        hub_params["overlay_by"] = ["samplename", "method", "norm"]
+        hub_params["subgroup_by"] = ["method", "norm", "strand"]
 
     return hub_params
 

diff --git a/seqnado/workflow/scripts/create_hub.py b/seqnado/workflow/scripts/create_hub.py
@@ -33,12 +33,12 @@ def get_rna_samplename(path: str):
 
 elif snakemake.params.assay == "ATAC":
     df["samplename"] = df["fn"].str.extract(r".*/(.*)\.(?:bigBed|bigWig)")
-    df["pileup_method"] = df["fn"].apply(lambda x: x.split("/")[-3])
+    df["method"] = df["fn"].apply(lambda x: x.split("/")[-3])
     df["norm"] = df["fn"].apply(lambda x: x.split("/")[-2])
 
 elif snakemake.params.assay == "RNA":
     df["samplename"] = df["fn"].apply(get_rna_samplename)
-    df["pileup_method"] = df["fn"].apply(lambda x: x.split("/")[-3])
+    df["method"] = df["fn"].apply(lambda x: x.split("/")[-3])
     df["strand"] = np.where(df["fn"].str.contains("_plus.bigWig"), "plus", "minus")
     df["norm"] = df["fn"].apply(lambda x: x.split("/")[-2])