From 5461df611eb9c743b017c74d0ae4935b4b65ac32 Mon Sep 17 00:00:00 2001
From: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com>
Date: Mon, 26 Feb 2024 16:06:10 +0100
Subject: [PATCH] bump also auto update nextclade version

---
 poreCov.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/poreCov.nf b/poreCov.nf
index d031738..3efc7cc 100755
--- a/poreCov.nf
+++ b/poreCov.nf
@@ -256,15 +256,15 @@ println "\033[0;33mWarning: Running --update might not be poreCov compatible!\03
         params.pangolindocker = "nanozoo/pangolin-v4:" + tagname
         println "\033[0;32mFound latest pangolin container, using: " + params.pangolindocker + " \033[0m" 
 
-        tagname = 'https://registry.hub.docker.com/v2/repositories/nanozoo/nextclade2/tags/'.toURL().text.split(',"name":"')[1].split('","')[0]
-        params.nextcladedocker = "nanozoo/nextclade2:" + tagname 
-        println "\033[0;32mFound latest nextclade2 container, using: " + params.nextcladedocker + " \033[0m"
+        tagname = 'https://registry.hub.docker.com/v2/repositories/nanozoo/nextclade3/tags/'.toURL().text.split(',"name":"')[1].split('","')[0]
+        params.nextcladedocker = "nanozoo/nextclade3:" + tagname 
+        println "\033[0;32mFound latest nextclade3 container, using: " + params.nextcladedocker + " \033[0m"
     } 
     if ( internetcheck.toString() == "false" ) { 
         println "\033[0;33mCould not find the latest pangolin container, trying: " + params.defaultpangolin + "\033[0m"
         params.pangolindocker = params.defaultpangolin 
 
-        println "\033[0;33mCould not find the latest nextclade2 container, trying: " + params.defaultnextclade + "\033[0m"
+        println "\033[0;33mCould not find the latest nextclade3 container, trying: " + params.defaultnextclade + "\033[0m"
         params.nextcladedocker = params.defaultnextclade 
     } 
 }