From 8cad32859691ca8567d2f013617a90db686ca01a Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Tue, 17 Oct 2023 15:33:23 +0200
Subject: [PATCH] updates

---
 resources/auxiliary_workflows/benchmark/workflow/Snakefile | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/resources/auxiliary_workflows/benchmark/workflow/Snakefile b/resources/auxiliary_workflows/benchmark/workflow/Snakefile
index 72e498ea..20861ae7 100644
--- 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"