From 332e8f7b30a4d6095d52bb8beaa08e93ae8e3d18 Mon Sep 17 00:00:00 2001
From: Zohaib Anwar <zohaib_anwar@ymail.com>
Date: Wed, 1 Mar 2023 20:42:23 +0000
Subject: [PATCH 1/2] add LOS to snpeff filtering criteria

---
 bin/functions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/functions.py b/bin/functions.py
index 46f6fc5..5393475 100755
--- a/bin/functions.py
+++ b/bin/functions.py
@@ -45,7 +45,7 @@ def select_snpeff_records(eff_string, ao_count):
     eff_list = eff_string.split(",")
 
     # if any records in the row contain '|p.', take only those records
-    EFF_records_list = [s for s in eff_list if '|p.' in s]
+    EFF_records_list = [s for s in eff_list if '|p.' or 'LOF' in s]
 
     # if no records contain '|p.', take the "intergenic" record
     if len(EFF_records_list) == 0:

From 87b06c68a8541c2f49d9df505192ccedd8b0cbc7 Mon Sep 17 00:00:00 2001
From: Zohaib Anwar <zohaib_anwar@ymail.com>
Date: Wed, 1 Mar 2023 20:42:48 +0000
Subject: [PATCH 2/2] conda timeout time increased

---
 conf/profiles.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/profiles.config b/conf/profiles.config
index 173f487..0abfe9a 100644
--- a/conf/profiles.config
+++ b/conf/profiles.config
@@ -7,6 +7,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        conda.createTimeout    = '1 h'
         includeConfig 'conda.config'
     }
     mamba {