updates

cbg-ethz · Oct 17, 2023 · 8cad328 · 8cad328
1 parent d99418d
commit 8cad328
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/resources/auxiliary_workflows/benchmark/workflow/Snakefile b/resources/auxiliary_workflows/benchmark/workflow/Snakefile
@@ -462,6 +462,7 @@ rule provide_real_data:
         parts=(${{tmp//@/ }})
         source="${{parts[0]}}"
         subsample_frac="{wildcards.coverage}"
+        subsample_frac="{wildcards.haplos}"
         echo "Using $subsample_frac of $source"
 
         mkdir -p "{output.dname_work}"
@@ -523,8 +524,9 @@ rule samtools_index:
         "envs/split.yaml"
     shell:
         """
-        samtools index {input} -o {output}
+        samtools index {input}
         """
+# samtools index {input} -o {output}
 
 
 rule read_statistics:
@@ -735,6 +737,6 @@ rule performance_measures_global:
     threads: 10
     resources:
         mem_mb=500,
-        runtime=60 * 24,
+        runtime=60 * 4,
     script:
         "scripts/performance_measures_global.py"