new threads

Clinical-Genomics · mathiasbio · Oct 11, 2024 · Jun 14, 2024 · Jun 14, 2024 · Jun 14, 2024
commit 3d44b03941eb50ef6c7be1a889535db9da914854
diff --git a/BALSAMIC/constants/cluster_analysis.json b/BALSAMIC/constants/cluster_analysis.json
@@ -156,6 +156,10 @@
 		"time": "24:00:00",
 		"n": 36
 	},
+	"sentieon_DNAscope_gnomad_tga": {
+		"time": "24:00:00",
+		"n": 12
+	},
 	"sentieon_TNhaplotyper": {
 		"time": "24:00:00",
 		"n": 36

diff --git a/BALSAMIC/snakemake_rules/variant_calling/gens_preprocessing.rule b/BALSAMIC/snakemake_rules/variant_calling/gens_preprocessing.rule
@@ -112,7 +112,7 @@ else:
         benchmark:
             Path(benchmark_dir,"sentieon_DNAscope_gnomad_{sample}.tsv").as_posix()
         threads:
-            get_threads(cluster_config,"sentieon_DNAscope_gnomad")
+            get_threads(cluster_config,"sentieon_DNAscope_gnomad_tga")
         message:
             "Calling germline variants on positions in Gnomad AF > 0.05 using Sentieon DNAscope for {params.sample}"
         shell:

diff --git a/BALSAMIC/utils/io.py b/BALSAMIC/utils/io.py

 def read_csv(csv_path: str, delimeter: str) -> List[dict]:
    """Read data from a csv file."""
    with open(csv_path, mode='r') as csv_file:
        csv_reader = csv.DictReader(csv_file, delimiter=delimeter)
        return [row for row in csv_reader]

 def read_yaml(yaml_path: str) -> dict:
    """Read data from a yaml file."""

	def read_csv(csv_path: str, delimeter: str) -> List[dict]:
	"""Read data from a csv file."""
	with open(csv_path, mode='r') as csv_file:
	csv_reader = csv.DictReader(csv_file, delimiter=delimeter)
	return [row for row in csv_reader]
Check warning on line 74 in BALSAMIC/utils/io.py Codecov / codecov/patch BALSAMIC/utils/io.py#L72-L74 `Added lines #L72 - L74 were not covered by tests`

	def read_yaml(yaml_path: str) -> dict:
	"""Read data from a yaml file."""