From 044cd22c6ec1628b1c7d310b0ad3c3ecc9a64be7 Mon Sep 17 00:00:00 2001
From: Daniel Park <dpark@broadinstitute.org>
Date: Thu, 19 Sep 2024 14:55:11 -0400
Subject: [PATCH 1/2] refine_assembly -- update to sanitize fasta headers

---
 assembly.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/assembly.py b/assembly.py
index 145f72b6..7f15a96e 100755
--- a/assembly.py
+++ b/assembly.py
@@ -915,9 +915,10 @@ def refine_assembly(
     novoalign = tools.novoalign.NovoalignTool(license_path=novoalign_license_path)
     gatk = tools.gatk.GATKTool(path=gatk_path)
 
-    # Create deambiguated genome for GATK
+    # Sanitize fasta header & create deambiguated genome for GATK
     deambigFasta = util.file.mkstempfname('.deambig.fasta')
-    deambig_fasta(inFasta, deambigFasta)
+    with util.file.fastas_with_sanitized_ids(inFasta, use_tmp=True) as sanitized_fastas:
+        deambig_fasta(sanitized_fastas[0], deambigFasta)
     picard_index.execute(deambigFasta, overwrite=True)
     samtools.faidx(deambigFasta, overwrite=True)
 

From f0685b4fcc885d2e4f366fd59a1af3d98baa83cc Mon Sep 17 00:00:00 2001
From: Daniel Park <dpark@broadinstitute.org>
Date: Thu, 19 Sep 2024 21:29:52 -0400
Subject: [PATCH 2/2] bump viral-core to 2.3.6

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index e04a953d..a5e3b92e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.3.5
+FROM quay.io/broadinstitute/viral-core:2.3.6
 
 LABEL maintainer "viral-ngs@broadinstitute.org"