Merge pull request #226 from UPHL-BioNGS/update-20240906

Update 20240906

Author: erinyoung

modules/local/amrfinderplus.nf

@@ -2,7 +2,7 @@ process amrfinderplus {
   tag           "${meta.id}"
   label         "process_high"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/ncbi-amrfinderplus:3.12.8-2024-05-02.2'
+  container     'staphb/ncbi-amrfinderplus:3.12.8-2024-07-22.1'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '30m'
 

modules/local/elgato.nf

@@ -2,7 +2,7 @@ process elgato {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/elgato:1.18.2'
+  container     'staphb/elgato:1.19.0'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

modules/local/mlst.nf

@@ -2,7 +2,7 @@ process mlst {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/mlst:2.23.0-2024-08-01'
+  container     'staphb/mlst:2.23.0-2024-09-01'
   maxForks      10
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'

nextflow.config

@@ -3,7 +3,7 @@ manifest {
   author                          = 'Erin Young'
   homePage                        = 'https://github.com/UPHL-BioNGS/Grandeur'
   mainScript                      = 'main.nf'
-  version                         = '4.5.24219'
+  version                         = '4.5.24250'
   defaultBranch                   = 'main'
   description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
   nextflowVersion                 = '!>=22.10.1'