From 369a528c5355db33b2ea239ac8aa677674e3dfeb Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Fri, 17 Nov 2023 18:19:16 +0100
Subject: [PATCH] [method_def] viloca with posterior threshold

---
 .../resources/method_definitions/viloca_alpha_0.00001.py      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/resources/auxiliary_workflows/benchmark/resources/method_definitions/viloca_alpha_0.00001.py b/resources/auxiliary_workflows/benchmark/resources/method_definitions/viloca_alpha_0.00001.py
index f83020e9..e65d84a5 100644
--- a/resources/auxiliary_workflows/benchmark/resources/method_definitions/viloca_alpha_0.00001.py
+++ b/resources/auxiliary_workflows/benchmark/resources/method_definitions/viloca_alpha_0.00001.py
@@ -2,6 +2,7 @@
 # CONDA: libshorah
 # CONDA: pyvcf
 # CONDA: biopython = 1.79
+# PIP: pandas
 # PIP: git+https://github.com/LaraFuhrmann/shorah@master
 
 import subprocess
@@ -12,6 +13,7 @@
 import gzip
 from fuc import pyvcf
 import pandas as pd
+import shutil
 
 
 def gunzip(source_filepath, dest_filepath, block_size=65536):
@@ -132,7 +134,7 @@ def main(
 
             elif file.endswith(".fas"):
                 fname_haplos = (dname_work / "support" / onlyfiles[0]).resolve()
-                (dname_work / "support" / file).copy(fname_result_haplos)
+                shutil.copy((dname_work / "support" / file).resolve(), fname_result_haplos)
 
     # fix frequency information