Merge pull request #238 from UPHL-BioNGS/update-241105

Update 241105
UPHL-BioNGS · Nov 7, 2024 · ca81699 · ca81699
2 parents db7a6cb + d910aa4
commit ca81699
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Showing 7 changed files with 10 additions and 10 deletions.
diff --git a/modules/local/blast.nf b/modules/local/blast.nf
@@ -2,7 +2,7 @@ process blastn {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/blast:2.15.0'
+  container     'staphb/blast:2.16.0'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '2h'
 

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:16.22.1'
+  container     'staphb/ncbi-datasets:16.30.0'
   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:16.22.1'
+  container     'staphb/ncbi-datasets:16.30.0'
   time          '5h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

diff --git a/modules/local/elgato.nf b/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:1.19.0'
+  container     'staphb/elgato:1.20.1'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

diff --git a/modules/local/iqtree2.nf b/modules/local/iqtree2.nf
@@ -2,7 +2,7 @@ process iqtree2 {
   tag           "Phylogenetic analysis"
   label         "process_high"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/iqtree2:2.3.1'
+  container     'staphb/iqtree2:2.3.6'
   time          '24h'
   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:2.23.0-2024-10-01'
+  container     'staphb/mlst:2.23.0-2024-11-01'
   maxForks      10
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'

diff --git a/modules/local/pbptyper.nf b/modules/local/pbptyper.nf
@@ -3,7 +3,7 @@ process pbptyper {
   label         "process_medium"
   stageInMode   "copy"
   publishDir    path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/pbptyper:1.0.4'
+  container     'staphb/pbptyper:2.0.0'
   time          '1h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
@@ -27,7 +27,7 @@ process pbptyper {
     log_file=logs/${task.process}/${prefix}.${workflow.sessionId}.log
     
     pbptyper ${args} \
-      --assembly ${contigs} \
+      --input ${contigs} \
       --prefix ${prefix} \
       --outdir pbptyper \
       | tee -a \$log_file
@@ -37,4 +37,4 @@ process pbptyper {
         pbptyper: \$(echo \$(pbptyper --version 2>&1) | sed 's/^.*pbptyper, version //;' )
     END_VERSIONS
   """
-}
+}
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                         = '4.5.24276'
+  version                         = '4.5.24310'
   defaultBranch                   = 'main'
   description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
   nextflowVersion                 = '!>=22.10.1'