From 1326f6206ca1201c2cb4a19de80c0ad7d25988d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolai=20von=20K=C3=BCgelgen?=
 <nicolai.von-kuegelgen@bih-charite.de>
Date: Fri, 23 Feb 2024 12:34:34 +0100
Subject: [PATCH] fix post_germline_calls_case_mode

---
 .../wrappers/gcnv/post_germline_calls_case_mode/wrapper.py    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py b/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py
index 41b03b9af..c53e89fa0 100644
--- a/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py
+++ b/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py
@@ -29,8 +29,8 @@
     exit 1
 fi
 
-# Get contig name style
-tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_${{sample_index}}/contig_ploidy.tsv | grep "chr" > /dev/null && true
+# Get contig name style; SAMPLE_0  is guaranteed to exist
+tail -n +2 $(dirname {snakemake.input.ploidy})/ploidy-calls/SAMPLE_0/contig_ploidy.tsv | grep "chr" > /dev/null && true
 exit_status=$?
 if [[ $exit_status == 0 ]]; then
     STYLE="chr"