perf: Tweak resources and bump version (#2)

Author: fgvieira

workflow/Snakefile

@@ -1,7 +1,7 @@
-snakemake.utils.min_version("8.11.2")
+snakemake.utils.min_version("9.0.0")
 
 # Define wrapper versions
-wrapper_ver = "v5.8.3"
+wrapper_ver = "v5.10.0"
 
 
 include: "rules/utils.smk"

workflow/rules/raw.smk

@@ -82,6 +82,6 @@ rule fastqc_raw:
     resources:
         # Memory is hard-coded to 250M per thread (https://github.com/bcbio/bcbio-nextgen/issues/2989)
         mem=lambda w, threads: f"{512* threads} MiB",
-        runtime=lambda w, attempt: f"{1* attempt} h",
+        runtime=lambda w, attempt: f"{2* attempt} h",
     wrapper:
         f"{wrapper_ver}/bio/fastqc"

workflow/rules/trim.smk

@@ -132,7 +132,7 @@ elif config["reads"]["trim"]["tool"] == "adapterremoval":
         threads: 10
         resources:
             mem=lambda w, attempt: f"{15* attempt} GiB",
-            runtime=lambda w, attempt: f"{2* attempt} h",
+            runtime=lambda w, attempt: f"{3* attempt} h",
         wrapper:
             f"{wrapper_ver}/bio/adapterremoval"
 

workflow/rules/utils.smk

@@ -9,23 +9,6 @@ from typing import List, Dict
 ### General
 
 
-def flatten(list_of_lists: List) -> List:
-    """Flatten an irregular list of lists recursively
-
-    https://stackoverflow.com/a/53778278
-
-    :param list_of_lists: A list of lists
-    :return result: A string that has been flattened from a list of lists
-    """
-    result = list()
-    for i in list_of_lists:
-        if isinstance(i, list):
-            result.extend(flatten(i))
-        else:
-            result.append(str(i))
-    return result
-
-
 def expand_pandas(string: List, df: pd.DataFrame, allow_missing=False) -> List:
     """Expand string following columns in the dataframe"""
     return set(