From 5981376ec9f725be6bd7d553fac3efbcb83c1969 Mon Sep 17 00:00:00 2001
From: AroneyS <samuel.aroney@qut.edu.au>
Date: Mon, 6 Jan 2025 11:26:35 +1000
Subject: [PATCH] disable sra after update downloads

---
 binchicken/binchicken.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/binchicken/binchicken.py b/binchicken/binchicken.py
index 2742354f..1b06e155 100755
--- a/binchicken/binchicken.py
+++ b/binchicken/binchicken.py
@@ -789,6 +789,11 @@ def update(args):
     else:
         sample_read_size = None
 
+    if args.sra:
+        args.forward, args.reverse = download_sra(args)
+        args.run_qc = True
+        args.sra = False
+
     if args.run_aviary:
         args.snakemake_args = "aviary_combine summary --rerun-triggers mtime " + args.snakemake_args if args.snakemake_args else "aviary_combine summary --rerun-triggers mtime"
     else:
@@ -1092,6 +1097,7 @@ def build(args):
     args.aviary_assemble_cores = None
     args.aviary_recover_cores = None
     args.assemble_unmapped = True
+    args.sra = False
     args.run_qc = True
     args.coassemblies = None
     args.coassemblies_list = None