From 82bcd41c0711f1596908432ecba42cf3325bde9c Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 31 Oct 2023 11:39:34 -0600
Subject: [PATCH 1/4] Update freyja to 1.4.7-2023-10-31

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

diff --git a/modules/freyja.nf b/modules/freyja.nf
index cb48861..a67f89b 100644
--- a/modules/freyja.nf
+++ b/modules/freyja.nf
@@ -3,7 +3,7 @@ process freyja {
   label         "process_medium"
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   publishDir    "${params.outdir}", mode: 'copy'
-  container     'quay.io/uphl/freyja:1.4.7-2023-10-24'
+  container     'quay.io/uphl/freyja:1.4.7-2023-10-31'
 
   //#UPHLICA maxForks 10
   //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
@@ -57,7 +57,7 @@ process freyja_aggregate {
   tag        "Aggregating results from freyja"
   label      "process_single"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'quay.io/uphl/freyja:1.4.7-2023-10-24'
+  container  'quay.io/uphl/freyja:1.4.7-2023-10-31'
 
   //#UPHLICA maxForks 10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

From 7c214b9bcf7989c89e983e40d196bce306fc9f94 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 31 Oct 2023 12:44:23 -0600
Subject: [PATCH 2/4] Update version to 3.8.20231031

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

diff --git a/nextflow.config b/nextflow.config
index 7a272c9..795d98d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
   name              = 'Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.8.20231024'
+  version           = 'v3.8.20231031'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'

From 187c266ebcfaad9d7c3888f6dcb0fbb862f0d588 Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 31 Oct 2023 12:45:47 -0600
Subject: [PATCH 3/4] log files from ivar trim std err

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

diff --git a/modules/ivar.nf b/modules/ivar.nf
index e06257d..1955806 100644
--- a/modules/ivar.nf
+++ b/modules/ivar.nf
@@ -138,7 +138,7 @@ process ivar_trim {
     # trimming the reads
     ivar trim !{params.ivar_trim_options} -e -i !{bam} -b !{primer_bed} -p ivar_trim/!{sample}.primertrim | tee -a $log
 
-    if [ -S "$log" ] ; then grep "Found" -A 10000 $log | grep -A 10000 "primers in BED file" > ivar_trim/!{sample}_ivar.log ; else touch ivar_trim/!{sample}_ivar.log ; fi
+    if [ -S "$log" ] ; then grep "Found" -A 10000 $log | grep -A 10000 "primers in BED file" 2> ivar_trim/!{sample}_ivar.log ; else touch ivar_trim/!{sample}_ivar.log ; fi
     
     # sorting and indexing the trimmed bams
     samtools sort ivar_trim/!{sample}.primertrim.bam -o ivar_trim/!{sample}.primertrim.sorted.bam | tee -a $log

From 844c6f79e8aa4882a3248e9d831bb53246365a8a Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 31 Oct 2023 12:48:41 -0600
Subject: [PATCH 4/4] Update pangolin to version 4.3.1-pdata-1.23.1

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

diff --git a/modules/pangolin.nf b/modules/pangolin.nf
index 34633f2..72b778b 100644
--- a/modules/pangolin.nf
+++ b/modules/pangolin.nf
@@ -2,7 +2,7 @@ process pangolin {
   tag        "SARS-CoV-2 lineage Determination"
   label      "process_medium"
   publishDir "${params.outdir}", mode: 'copy'
-  container  'staphb/pangolin:4.3.1-pdata-1.22'
+  container  'staphb/pangolin:4.3.1-pdata-1.23.1'
 
   //#UPHLICA maxForks      10
   //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}