From 8358e45d8ca1a097a36176b7f3a543cd9fab9a8b Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Fri, 6 Sep 2024 13:41:00 -0600
Subject: [PATCH 1/4] Update to 4.5.24250

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

diff --git a/nextflow.config b/nextflow.config
index 72d59e1..621fb64 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                         = '4.5.24219'
+  version                         = '4.5.24250'
   defaultBranch                   = 'main'
   description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
   nextflowVersion                 = '!>=22.10.1'

From 18ec2af14853b82789e4df62daf0a59466a4486e Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Fri, 6 Sep 2024 13:41:31 -0600
Subject: [PATCH 2/4] Update amrfinder to 3.12.8-2024-07-22.1

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

diff --git a/modules/local/amrfinderplus.nf b/modules/local/amrfinderplus.nf
index 2d21f9a..e921e20 100644
--- a/modules/local/amrfinderplus.nf
+++ b/modules/local/amrfinderplus.nf
@@ -2,7 +2,7 @@ process amrfinderplus {
   tag           "${meta.id}"
   label         "process_high"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/ncbi-amrfinderplus:3.12.8-2024-05-02.2'
+  container     'staphb/ncbi-amrfinderplus:3.12.8-2024-07-22.1'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '30m'
 

From 64206548b2aeac16289b2a37c95643ad8373b568 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Fri, 6 Sep 2024 13:42:01 -0600
Subject: [PATCH 3/4] Update elgato to 1.19.0

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

diff --git a/modules/local/elgato.nf b/modules/local/elgato.nf
index 22dadaa..d5e33a8 100755
--- 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:1.18.2'
+  container     'staphb/elgato:1.19.0'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

From 0581d8e6571195ab2a472d2f53b4d5b18d8cb6be Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Fri, 6 Sep 2024 13:42:48 -0600
Subject: [PATCH 4/4] Update mlst to 2.23.0-2024-09-01

---
 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 352e0c3..5f0701c 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:2.23.0-2024-08-01'
+  container     'staphb/mlst:2.23.0-2024-09-01'
   maxForks      10
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'