Merge pull request #273 from UPHL-BioNGS/update-20250507

Update 20250507

Author: erinyoung

modules/local/amrfinderplus.nf

@@ -1,7 +1,7 @@
 process AMRFINDER {
   tag           "${meta.id}"
   label         "process_high"
-  container     'staphb/ncbi-amrfinderplus:4.0.19-2024-12-18.1'
+  container     'staphb/ncbi-amrfinderplus:4.0.22-2025-03-25.1'
 
   input:
   tuple val(meta), file(contigs), val(genus), val(species)

modules/local/elgato.nf

@@ -1,7 +1,7 @@
 process ELGATO {
   tag           "${meta.id}"
   label         "process_medium"
-  container     'staphb/elgato:1.21.0'
+  container     'staphb/elgato:1.21.2'
 
   input:
   tuple val(meta), file(contigs)

modules/local/fastp.nf

@@ -1,7 +1,7 @@
 process FASTP {
   tag           "${meta.id}"
   label         "process_low"
-  container     'staphb/fastp:0.24.0'
+  container     'staphb/fastp:0.24.1'
 
   input:
   tuple val(meta), file(reads)

modules/local/kraken2.nf

@@ -1,7 +1,7 @@
 process KRAKEN2 {
   tag           "${meta.id}"
   label         "process_high"
-  container     'staphb/kraken2:2.1.3'
+  container     'staphb/kraken2:2.1.5'
 
   input:
   tuple val(meta), file(fastq), path(kraken2_db)

modules/local/multiqc.nf

@@ -1,7 +1,7 @@
 process MULTIQC {
   tag           "multiqc"
   label         "process_single"
-  container     'staphb/multiqc:1.27.1'
+  container     'staphb/multiqc:1.28'
 
   input:
   file(input)
@@ -60,4 +60,4 @@ process VERSIONS {
 
     python3 ${versions_script}
   """
-}
+}

nextflow.config

@@ -196,7 +196,7 @@ manifest {
   author                          = 'Erin Young'
   homePage                        = 'https://github.com/UPHL-BioNGS/Grandeur'
   mainScript                      = 'main.nf'
-  version                         = '4.9.25098'
+  version                         = '4.9.25127'
   defaultBranch                   = 'main'
   description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
   nextflowVersion                 = '!>=24.04.4'