Merge pull request #257 from UPHL-BioNGS/update-20231121

Update 20231121
UPHL-BioNGS · Nov 21, 2023 · 799a261 · 799a261
2 parents af3f923 + 5d2a3ee
commit 799a261
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Showing 3 changed files with 15 additions and 15 deletions.
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    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.7-2023-11-14'
+  container     'quay.io/uphl/freyja:1.4.7-2023-11-21'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -44,7 +44,7 @@ process freyja_demix {
   label         "process_medium"
   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.7-2023-11-14'
+  container     'quay.io/uphl/freyja:1.4.7-2023-11-21'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -85,7 +85,7 @@ process freyja_boot {
   label         "process_medium"
   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.7-2023-11-14'
+  container     'quay.io/uphl/freyja:1.4.7-2023-11-21'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -124,7 +124,7 @@ process freyja_aggregate {
   tag        "Aggregating results from freyja"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'quay.io/uphl/freyja:1.4.7-2023-11-14'
+  container  'quay.io/uphl/freyja:1.4.7-2023-11-21'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/samtools.nf b/modules/samtools.nf
@@ -2,7 +2,7 @@ process samtools_stats {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -37,7 +37,7 @@ process samtools_coverage {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -74,7 +74,7 @@ process samtools_flagstat {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -111,7 +111,7 @@ process samtools_depth {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -147,7 +147,7 @@ process samtools_ampliconstats {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -185,7 +185,7 @@ process samtools_plot_ampliconstats {
   label      "process_single"
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'staphb/samtools:1.17'
+  container     'staphb/samtools:1.18'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -221,7 +221,7 @@ process samtools_sort {
   tag        "${sample}"
   label      "process_high"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -258,7 +258,7 @@ process samtools_filter {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -300,7 +300,7 @@ process samtools_ampliconclip {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -340,7 +340,7 @@ process samtools_markdup {
   tag        "${sample}"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/samtools:1.17'
+  container  'staphb/samtools:1.18'
 
   //#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           = 'v3.10.20231115'
+  version           = 'v3.10.20231121'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'