From 8eae175bb2778dd48057b01bdd8e4063b40747cc Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Tue, 5 Nov 2024 15:26:24 -0700
Subject: [PATCH] Update pbptyper to 2.0.0

---
 modules/local/pbptyper.nf | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/local/pbptyper.nf b/modules/local/pbptyper.nf
index 9cb85d5..75a491e 100644
--- a/modules/local/pbptyper.nf
+++ b/modules/local/pbptyper.nf
@@ -3,7 +3,7 @@ process pbptyper {
   label         "process_medium"
   stageInMode   "copy"
   publishDir    path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/pbptyper:1.0.4'
+  container     'staphb/pbptyper:2.0.0'
   time          '1h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
@@ -27,7 +27,9 @@ process pbptyper {
     log_file=logs/${task.process}/${prefix}.${workflow.sessionId}.log
     
     pbptyper ${args} \
-      --assembly ${contigs} \
+      --yaml data/pbptyper.yaml \
+      --targets data/pbptyper.fasta \
+      --input ${contigs} \
       --prefix ${prefix} \
       --outdir pbptyper \
       | tee -a \$log_file
@@ -37,4 +39,4 @@ process pbptyper {
         pbptyper: \$(echo \$(pbptyper --version 2>&1) | sed 's/^.*pbptyper, version //;' )
     END_VERSIONS
   """
-}
\ No newline at end of file
+}