Merge pull request #393 from UPHL-BioNGS/update-20241210

Update 20241210 to 3.22.24345

.github/workflows/check_versions.yml

@@ -20,7 +20,7 @@ jobs:
       - name: versions
         run: |
           issue_text="Needing updates:  " 
-          workflow_containers=($(grep container modules/* | grep staphb | sort | uniq | grep -v latest | awk '{print $3}' | sed 's/'\''//g'))
+          workflow_containers=($(grep container modules/local/* | grep staphb | sort | uniq | grep -v latest | awk '{print $3}' | sed 's/'\''//g'))
           for container in ${workflow_containers[@]}
           do
             base=$(echo $container | cut -f 1 -d ":")
@@ -41,7 +41,7 @@ jobs:
           done
 
           latest_nextclade_version=$(docker run nextstrain/nextclade:latest nextclade --version | awk '{print $2}')
-          worfklow_nextclade_version=$(grep container modules/nextclade.nf | cut -f 2 -d ":" | cut -f 1 -d "'" | head -n 1)
+          worfklow_nextclade_version=$(grep container modules/local/nextclade.nf | cut -f 2 -d ":" | cut -f 1 -d "'" | head -n 1)
 
           if [[ "$latest_nextclade_version" == "$worfklow_nextclade_version" ]]
           then

modules/local/freyja.nf

@@ -1,7 +1,7 @@
 process FREYJA {
   tag           "${meta.id}"
   label         "process_medium"
-  container     'staphb/freyja:1.5.2-11_30_2024-02-00-2024-12-02'
+  container     'staphb/freyja:1.5.2-12_08_2024-01-33-2024-12-09'
 
   input:
   tuple val(meta), file(bam), file(reference_genome)
@@ -51,7 +51,7 @@ process FREYJA {
 process FREYJA_AGGREGATE {
   tag        "Aggregating results from freyja"
   label      "process_single"
-  container  'staphb/freyja:1.5.2-11_30_2024-02-00-2024-12-02'
+  container  'staphb/freyja:1.5.2-12_08_2024-01-33-2024-12-09'
 
   input:
   file(demix)

nextflow.config

@@ -259,11 +259,11 @@ dag {
 //########## manifest values     ##########
 manifest {
   mainScript        = 'main.nf'
-  nextflowVersion   = '>=22.10.7'
+  nextflowVersion   = '>=24.04.4'
   name              = 'UPHL-BioNGS/Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.22.24331'
+  version           = 'v3.22.24345'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'
@@ -284,4 +284,4 @@ validation {
 includeConfig 'conf/base.config'
 
 // Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+includeConfig 'conf/modules.config'