incorporated nextclade 2 changes

nextflow.config

@@ -46,8 +46,8 @@ params {
     lcs_ucsc_downsampling = 10000 // 'None' to turn off
     lcs_variant_groups = 'default' // 'default' to use file from repo; custom variant groups table for marker-table update
     lcs_cutoff = 0.03
-    defaultpangolin = 'nanozoo/pangolin-v4:4.0.4--1.2.133'
-    defaultnextclade = 'nanozoo/nextclade:1.11.0--2022-03-31'
+    defaultpangolin = 'nanozoo/pangolin-v4:4.1.1--1.11'
+    defaultnextclade = 'nanozoo/nextclade2:2.2.0--2022-06-14'
     scorpio = false
 
     // parameters
@@ -175,8 +175,10 @@ profiles {
         includeConfig 'configs/nodes.config'
 
         // cloud error strategy
-        process.errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'ignore' }
-        process.maxRetries = 3
-        process.executor = 'google-lifesciences'
+        process { 
+            errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'ignore' }
+            maxRetries = 3
+            executor = 'google-lifesciences'
         }
+    }
 }

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/nextclade/tags/'.toURL().text.split(',"name":"')[1].split('","')[0]
-        params.nextcladedocker = "nanozoo/nextclade:" + tagname 
-        println "\033[0;32mFound latest nextclade container, using: " + params.nextcladedocker + " \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"
     } 
     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 nextclade container, trying: " + params.defaultnextclade + "\033[0m"
+        println "\033[0;33mCould not find the latest nextclade2 container, trying: " + params.defaultnextclade + "\033[0m"
         params.nextcladedocker = params.defaultnextclade 
     } 
 }

workflows/process/nextclade.nf

@@ -8,7 +8,8 @@ process nextclade {
         tuple val(name), path("${name}_clade.tsv")
     script:
     """
-    nextclade run --input-fasta ${consensus} --input-dataset /data/sars-cov-2_MN908947 --output-tsv tmp.tsv
+    nextclade run -j ${task.cpus} --input-dataset /data/sars-cov-2_MN908947 --output-tsv tmp.tsv ${consensus}
+
     cat tmp.tsv | tr -d "\r" > ${name}_clade.tsv
     """
     stub: