From f35a63a315b70fdcb8aa6631c73f109f2d026cc3 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 6 Aug 2024 10:40:32 -0600
Subject: [PATCH 1/4] Update nextflow to 4.5.24219

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 6eeb5a4..72d59e1 100644
--- 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'

From 74a9990b254fca64b7d5ebd6556b2ee9696e90b3 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 6 Aug 2024 10:42:25 -0600
Subject: [PATCH 2/4] Update mlst to 2.23.0-2024-08-01

---
 modules/local/mlst.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/mlst.nf b/modules/local/mlst.nf
index 43b069b..352e0c3 100644
--- 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'

From 108e6d577c212fde6f36b2802c286fd7ace42777 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 6 Aug 2024 10:43:13 -0600
Subject: [PATCH 3/4] Update datasets to 16.22.1

---
 modules/local/datasets.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/datasets.nf b/modules/local/datasets.nf
index b1320ba..4ef6a81 100644
--- 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'}
   

From 3ffb6e3075c70cb90438530aeda2a0781d1c82cd Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 6 Aug 2024 10:43:40 -0600
Subject: [PATCH 4/4] Update spades to 4.0.0

---
 modules/local/spades.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/spades.nf b/modules/local/spades.nf
index be42087..138c97d 100644
--- 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'