fixes

src/harpy/helperfunctions.py

@@ -33,14 +33,13 @@ def generate_conda_deps():
     os.makedirs(".harpy_envs", exist_ok = True)
 
     for i in environ:
-        # don't overwrite existing
-        if not os.path.isfile(f".harpy_envs/{i}.yaml"):
-            with open(f".harpy_envs/{i}.yaml", "w") as yml:
-                yml.write(f"name: {i}\n")
-                yml.write("channels:\n  - ")
-                yml.write("\n  - ".join(condachannels))
-                yml.write("\ndependencies:\n  - ")
-                yml.write("\n  - ".join(environ[i]) + "\n")
+        # overwrites existing
+        with open(f".harpy_envs/{i}.yaml", "w") as yml:
+            yml.write(f"name: {i}\n")
+            yml.write("channels:\n  - ")
+            yml.write("\n  - ".join(condachannels))
+            yml.write("\ndependencies:\n  - ")
+            yml.write("\n  - ".join(environ[i]) + "\n")
 
 def fetch_script(workdir, target):
     """

src/harpy/reports/PreflightBam.Rmd

@@ -138,21 +138,6 @@ out of the zoomed view.
 
 ## datarow
 ### plot {.no-title}
-```{r status_df}
-data2 <- data %>% 
-  mutate(
-    nameMismatch = ifelse(nameMismatch > 0, "fail", "pass"),
-    noMI = ifelse(noMI == alignments, "fail", "pass"),
-    noBX = ifelse(noBX == alignments, "fail", "pass"),
-    badBX = ifelse(badBX > 0, "fail", "pass"),
-    bxNotLast = ifelse(bxNotLast > 0, "fail", "pass")
-    ) %>% 
-  select(-3) %>% 
-  #rename("1" = "nameMismatch", "2" = "noMI", "3" = "noBX", "4" = "badBX", "5" = "bxNotLast") %>% 
-  pivot_longer(-1, names_to = "category", values_to = "Status")
-#data2$category <- as.integer(data2$category)
-```
-
 ```{r status_df}
 data2 <- data %>% 
   mutate(