Merge pull request #99 from UPHL-BioNGS/update-20241105

Update donut_falls to latest software versions
UPHL-BioNGS · Nov 7, 2024 · 39ac777 · 39ac777
2 parents 54982d3 + 4408358
commit 39ac777
Showing 1 changed file with 13 additions and 13 deletions.
diff --git a/donut_falls.nf b/donut_falls.nf
@@ -162,7 +162,7 @@ process busco {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/busco:5.7.1-prok-bacteria_odb10_2024-01-08'
+  container     'staphb/busco:5.8.0-prok-bacteria_odb10_2024-01-08'
   time          '45m'
 
   input:
@@ -197,7 +197,7 @@ process bwa {
   tag           "${meta.id}"
   label         'process_high'
   // no publishDir because the sam files are too big
-  container     'staphb/bwa:0.7.17'
+  container     'staphb/bwa:0.7.18'
   time          '2h'
 
   input:
@@ -275,7 +275,7 @@ process copy {
   tag           "${meta.id}"
   label         'process_low'
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/multiqc:1.19'
+  container     'staphb/multiqc:1.25'
   time          '10m'
 
   input:
@@ -399,7 +399,7 @@ process dnaapler {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/dnaapler:0.7.0'
+  container     'staphb/dnaapler:0.8.1'
   time          '1h'
 
   input:
@@ -498,7 +498,7 @@ process flye {
   tag           "${meta.id}"
   label         "process_high"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/flye:2.9.4'
+  container     'staphb/flye:2.9.5'
   time          '10h'
 
   input:
@@ -588,7 +588,7 @@ process gfa_to_fasta {
   tag           "${meta.id}"
   label         "process_low"
   // no publishDir
-  container     'staphb/multiqc:1.19'
+  container     'staphb/multiqc:1.25'
   time          '10m'
 
   input:
@@ -740,7 +740,7 @@ process multiqc {
   tag           "combining reports"
   label         "process_low"
   publishDir    "${params.outdir}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/multiqc:1.19'
+  container     'staphb/multiqc:1.25'
   time          '10m'
 
   input:
@@ -996,7 +996,7 @@ process png {
   tag           "${meta.id}"
   label         "process_low"
   publishDir    "${params.outdir}/${meta.id}/bandage", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/multiqc:1.19'
+  container     'staphb/multiqc:1.25'
   time          '10m'
 
   input:
@@ -1160,7 +1160,7 @@ process rasusa {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/rasusa:2.0.0'
+  container     'staphb/rasusa:2.1.0'
   time          '10m'
 
   input:
@@ -1234,7 +1234,7 @@ process summary {
   tag           "Creating summary"
   label         "process_low"
   publishDir    "${params.outdir}/summary", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/multiqc:1.19'
+  container     'staphb/multiqc:1.25'
   time          '30m'
 
   input:
@@ -1548,7 +1548,7 @@ process versions {
   tag           "extracting versions"
   label         "process_low"
   publishDir    "${params.outdir}/summary", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/multiqc:1.19'
+  container     'staphb/multiqc:1.25'
   time          '30m'
 
   input:
@@ -1656,7 +1656,7 @@ process test {
   tag           "Downloading R10.4 reads"
   label         "process_low"
   publishDir    "${params.outdir}/test_files/", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/multiqc:1.19'
+  container     'staphb/gfastats:1.3.7'
   time          '1h'
 
   output:
@@ -1979,4 +1979,4 @@ workflow.onComplete {
   println("The consensus fasta files can be found in ${params.outdir}/sample/consensus")
   println("The fasta files are from each phase of assembly. polca > polypolish > medaka > unpolished")
   println("Execution status: ${ workflow.success ? 'OK' : 'failed' }")
-}
+}