Merge pull request #415 from UPHL-BioNGS/20250211

Update to 3.26.25042

.github/workflows/check_versions.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   check:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test.yml

@@ -6,7 +6,7 @@ run-name: Download fastq and fasta and run
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_kraken2.yml

@@ -6,7 +6,7 @@ run-name: Test profile
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_mpx.yml

@@ -6,7 +6,7 @@ run-name: MPX
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_mpx_idt.yml

@@ -6,7 +6,7 @@ run-name: MPX with IDT Primers
 
 jobs:
   mpx_idt:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_mpx_primalseq.yml

@@ -6,7 +6,7 @@ run-name: mpx_primalseq
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_mpx_yale.yml

@@ -6,7 +6,7 @@ run-name: mpx_yale
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_nanopore.yml

@@ -6,7 +6,7 @@ run-name: nanopore
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_primers.yml

@@ -6,11 +6,11 @@ run-name: primers
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         primer:
-          [
+          [ 
             "midnight_idt_V1",
             "midnight_ont_V1",
             "midnight_ont_V2",

.github/workflows/test_profile.yml

@@ -6,7 +6,7 @@ run-name: Test profile
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_profile1.yml

@@ -6,7 +6,7 @@ run-name: Profile 1
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_profile2.yml

@@ -6,7 +6,7 @@ run-name: Profile 2
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_profile3.yml

@@ -6,7 +6,7 @@ run-name: Profile 3
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_relatedness.yml

@@ -6,7 +6,7 @@ run-name: Test MSA
 
 jobs:
   msa:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_samplesheet.yml

@@ -6,7 +6,7 @@ run-name: Download fastq and fasta and run
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/test_wastewater.yml

@@ -6,7 +6,7 @@ run-name: Download wastewater fastq
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

.github/workflows/update_nextclade.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   update-nextclade-dataset:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@master

modules/local/freyja.nf

@@ -1,7 +1,7 @@
 process FREYJA {
   tag           "${meta.id}"
   label         "process_medium"
-  container     'staphb/freyja:1.5.2-02_03_2025-02-26-2025-02-03'
+  container     'staphb/freyja:1.5.2-02_10_2025-01-52-2025-02-10'
 
   input:
   tuple val(meta), file(bam), file(reference_genome)

nextflow.config

@@ -166,6 +166,17 @@ profiles {
     apptainer.enabled       = false
     docker.runOptions       = '-u $(id -u):$(id -g)'
   }
+  apptainer {
+    singularity.enabled     = false
+    singularity.autoMounts  = false
+    conda.enabled           = false
+    docker.enabled          = false
+    podman.enabled          = false
+    shifter.enabled         = false
+    charliecloud.enabled    = false
+    apptainer.enabled       = true
+    apptainer.autoMounts    = true
+  }
   singularity {
     singularity.enabled     = true
     singularity.autoMounts  = true
@@ -263,7 +274,7 @@ manifest {
   name              = 'UPHL-BioNGS/Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.26.25034'
+  version           = 'v3.26.25042'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'