From e5b111d6486b61b05b19c6065fce33fefbdd11a9 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:05:13 -0700
Subject: [PATCH 1/8] Update to 4.9.25035

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

diff --git a/nextflow.config b/nextflow.config
index 146d605..2618412 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -196,7 +196,7 @@ manifest {
   author                          = 'Erin Young'
   homePage                        = 'https://github.com/UPHL-BioNGS/Grandeur'
   mainScript                      = 'main.nf'
-  version                         = '4.9.24345'
+  version                         = '4.9.25035'
   defaultBranch                   = 'main'
   description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
   nextflowVersion                 = '!>=24.04.4'

From 6cff8453a7535ad8a8dd68d341aa71070c2a0ce9 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:06:25 -0700
Subject: [PATCH 2/8] Update bakta to 1.10.3-5.1-light

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

diff --git a/modules/local/bakta.nf b/modules/local/bakta.nf
index 2dde20b..4fe5ae6 100644
--- a/modules/local/bakta.nf
+++ b/modules/local/bakta.nf
@@ -1,7 +1,7 @@
 process BAKTA {
   tag           "${meta.id}"
   label         "process_high"
-  container     'staphb/bakta:1.9.4-5.1-light'
+  container     'staphb/bakta:1.10.3-5.1-light'
   time    '30m'
 
   input:

From d8668926e5f9841f031e4ad24cfaf7ac7cc2bcf5 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:06:50 -0700
Subject: [PATCH 3/8] Update elgato to 1.20.2

---
 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 d2814ec..620384c 100755
--- a/modules/local/elgato.nf
+++ b/modules/local/elgato.nf
@@ -1,7 +1,7 @@
 process ELGATO {
   tag           "${meta.id}"
   label         "process_medium"
-  container     'staphb/elgato:1.20.1'
+  container     'staphb/elgato:1.20.2'
 
   input:
   tuple val(meta), file(contigs)

From 7b38f78d7c3248bab2640bb872791a9bd4c50b12 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:07:20 -0700
Subject: [PATCH 4/8] Update fastp to 0.24.0

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

diff --git a/modules/local/fastp.nf b/modules/local/fastp.nf
index e0c04d6..d0bf7c5 100644
--- a/modules/local/fastp.nf
+++ b/modules/local/fastp.nf
@@ -1,7 +1,7 @@
 process FASTP {
   tag           "${meta.id}"
   label         "process_low"
-  container     'staphb/fastp:0.23.4'
+  container     'staphb/fastp:0.24.0'
   
   input:
   tuple val(meta), file(reads)

From dba0c299f04af6e02383c1b5d7edd38274928846 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:08:01 -0700
Subject: [PATCH 5/8] Update mlst to 2.23.0-2025-02-01

---
 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 0a6df2e..9aa79ef 100644
--- a/modules/local/mlst.nf
+++ b/modules/local/mlst.nf
@@ -1,7 +1,7 @@
 process MLST {
   tag           "${meta.id}"
   label         "process_medium"
-  container     'staphb/mlst:2.23.0-2025-01-01'
+  container     'staphb/mlst:2.23.0-2025-02-01'
 
   input:
   tuple val(meta), file(contig), file(script)

From 1b536d91e11ca5ff49f2e19e4b7a015a44555579 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:08:41 -0700
Subject: [PATCH 6/8] Update amrfinderplus to 4.0.15-2024-12-18.1

---
 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 c26fecd..6e1b4f2 100644
--- a/modules/local/amrfinderplus.nf
+++ b/modules/local/amrfinderplus.nf
@@ -1,7 +1,7 @@
 process AMRFINDER {
   tag           "${meta.id}"
   label         "process_high"
-  container     'staphb/ncbi-amrfinderplus:4.0.3-2024-10-22.1'
+  container     'staphb/ncbi-amrfinderplus:4.0.15-2024-12-18.1'
 
   input:
   tuple val(meta), file(contigs), val(genus), val(species)

From 04a4d8ca503a7b010ee5f219b7cf6e82e6741458 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:09:03 -0700
Subject: [PATCH 7/8] Update datasets to 16.38.1

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

diff --git a/modules/local/datasets.nf b/modules/local/datasets.nf
index 288097f..ca7fe53 100644
--- a/modules/local/datasets.nf
+++ b/modules/local/datasets.nf
@@ -1,7 +1,7 @@
 process DATASETS_SUMMARY {
   tag           "${taxon}"
   label         "process_single"
-  container     'staphb/ncbi-datasets:16.35.0'
+  container     'staphb/ncbi-datasets:16.38.1'
 
   input:
   tuple val(taxon), file(script)

From f1dee4785b01bbbbf59881c39b89400ccd8c4fe7 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 4 Feb 2025 10:09:27 -0700
Subject: [PATCH 8/8] Update panaroo to 1.5.1

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

diff --git a/modules/local/panaroo.nf b/modules/local/panaroo.nf
index 7252677..5968342 100755
--- a/modules/local/panaroo.nf
+++ b/modules/local/panaroo.nf
@@ -1,7 +1,7 @@
 process PANAROO {
   tag           "Core Genome Alignment"
   label         "process_high"
-  container     'staphb/panaroo:1.5.0'
+  container     'staphb/panaroo:1.5.1'
   
   input:
   file(gff)