Merge pull request #220 from UPHL-BioNGS/update-20240806

Update 20240806
UPHL-BioNGS · Aug 6, 2024 · b4bf882 · b4bf882
2 parents 5b76ca4 + 3ffb6e3
commit b4bf882
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/modules/local/datasets.nf b/modules/local/datasets.nf
@@ -2,7 +2,7 @@ process datasets_summary {
   tag           "${taxon}"
   label         "process_single"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/ncbi-datasets:16.15.0'
+  container     'staphb/ncbi-datasets:16.22.1'
   time          '1h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore' }
 
@@ -52,7 +52,7 @@ process datasets_download {
   // because there's no way to specify threads
   label         "process_medium"
   publishDir    path: "${params.outdir}", mode: 'copy', pattern: "logs/*/*log"
-  container     'staphb/ncbi-datasets:16.15.0'
+  container     'staphb/ncbi-datasets:16.22.1'
   time          '5h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

diff --git a/modules/local/mlst.nf b/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:2.23.0-2024-06-01'
+  container     'staphb/mlst:2.23.0-2024-08-01'
   maxForks      10
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'

diff --git a/modules/local/spades.nf b/modules/local/spades.nf
@@ -5,7 +5,7 @@ process spades {
   publishDir    path: params.outdir, mode: 'copy', pattern: 'spades/*'
   publishDir    path: params.outdir, mode: 'copy', pattern: 'spades/*/*'
   publishDir    path: params.outdir, mode: 'copy', pattern: 'contigs/*'
-  container     'staphb/spades:3.15.5'
+  container     'staphb/spades:4.0.0'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '5h'
 

diff --git a/nextflow.config b/nextflow.config
@@ -3,7 +3,7 @@ manifest {
   author                          = 'Erin Young'
   homePage                        = 'https://github.com/UPHL-BioNGS/Grandeur'
   mainScript                      = 'main.nf'
-  version                         = '4.5.24184'
+  version                         = '4.5.24219'
   defaultBranch                   = 'main'
   description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
   nextflowVersion                 = '!>=22.10.1'