From d3e7657dd912eb5e0219a7e949857499b0cd1cc4 Mon Sep 17 00:00:00 2001
From: Thomas Weber <thomas.weber@embl.de>
Date: Tue, 2 Jul 2024 07:56:59 +0000
Subject: [PATCH] fix(startup): Fix wrongly placed config for paired_end
 parameter in common.smk

---
 workflow/rules/common.smk | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index cd36d01..1bc6ec5 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -4,6 +4,12 @@ import collections
 import yaml
 import subprocess
 
+
+if config["paired_end"] is True:
+    pair = ["1", "2"]
+else:
+    pair = ["1"]
+
 if config["mosaicatcher_pipeline"] == False:
     exclude = [
         "._.DS_Store",
@@ -40,11 +46,6 @@ if config["mosaicatcher_pipeline"] == False:
             "chr" + str(e) for e in list(range(1, 20)) + ["X", "Y"]
         ]
 
-    if config["paired_end"] is True:
-        pair = ["1", "2"]
-    else:
-        pair = ["1"]
-
     from scripts.utils import pipeline_aesthetic_start_ashleys
 
     if config["list_commands"] is True:
@@ -483,7 +484,7 @@ def get_final_output(wildcards):
     if config["publishdir"] != "":
         final_list.extend(
             expand(
-                "{folder}/{sample}/config/publishdir_outputs.ok",
+                "{folder}/{sample}/config/publishdir_outputs_ashleys.ok",
                 folder=config["data_location"],
                 sample=wildcards.sample,
             )