Merge pull request #332 from UPHL-BioNGS/update-20240521

Update 20240521
UPHL-BioNGS · May 21, 2024 · 606dece · 606dece
2 parents a3b709b + 78c165c
commit 606dece
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Showing 6 changed files with 9 additions and 9 deletions.
diff --git a/modules/artic.nf b/modules/artic.nf
@@ -26,7 +26,7 @@ process artic {
     path "versions.yml", emit: versions
 
     shell:
-    def args   = task.ext.args   ?: "${params.artic_options}}"
+    def args   = task.ext.args   ?: "${params.artic_options}"
     def prefix = task.ext.prefix ?: "${sample}"
     """
     mkdir -p artic consensus schema/cecret/V1 logs/${task.process}

diff --git a/modules/freyja.nf b/modules/freyja.nf
@@ -3,7 +3,7 @@ process freyja_variants {
   label         "process_medium"
   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/freyja:1.5.0-05_11_2024-01-10-2024-05-14'
+  container     'staphb/freyja:1.5.0-05_17_2024-01-06-2024-05-21'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -53,7 +53,7 @@ process freyja_demix {
   label         "process_medium"
   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/freyja:1.5.0-05_11_2024-01-10-2024-05-14'
+  container     'staphb/freyja:1.5.0-05_17_2024-01-06-2024-05-21'
 
 
   //#UPHLICA maxForks 10
@@ -105,7 +105,7 @@ process freyja_aggregate {
   tag        "Aggregating results from freyja"
   label      "process_single"
   publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container  'staphb/freyja:1.5.0-05_11_2024-01-10-2024-05-14'
+  container  'staphb/freyja:1.5.0-05_17_2024-01-06-2024-05-21'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/iqtree2.nf b/modules/iqtree2.nf
@@ -2,7 +2,7 @@ process iqtree2 {
   tag        "Creating phylogenetic tree with iqtree"
   label      "process_high"
   publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container  'staphb/iqtree2:2.2.2.7'
+  container  'staphb/iqtree2:2.3.1'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/minimap2.nf b/modules/minimap2.nf
@@ -24,7 +24,7 @@ process minimap2 {
   path "versions.yml", emit: versions
 
   shell:
-  def args   = task.ext.args   ?: "${params.minimap2_options}}"
+  def args   = task.ext.args   ?: "${params.minimap2_options}"
   def fastq  = reads.join(" ")
   def prefix = task.ext.prefix ?: "${sample}"
   """

diff --git a/modules/nextclade.nf b/modules/nextclade.nf
@@ -2,7 +2,7 @@ process nextclade_dataset {
   tag        "Downloading Dataset"
   label      "process_medium"
   publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container  'nextstrain/nextclade:3.4.0'
+  container  'nextstrain/nextclade:3.5.0'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -47,7 +47,7 @@ process nextclade {
   tag        "Clade Determination"
   label      "process_medium"
   publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container  'nextstrain/nextclade:3.4.0'
+  container  'nextstrain/nextclade:3.5.0'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/nextflow.config b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
   name              = 'Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.13.20240514'
+  version           = 'v3.14.240521'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'