support isolate mode but keep --careful as default

stajichlab · Jun 3, 2022 · 526fff0 · 526fff0
1 parent ceb06fa
commit 526fff0
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/AAFTF/AAFTF_main.py b/AAFTF/AAFTF_main.py
@@ -337,12 +337,13 @@ def main():
     parser_asm.add_argument('--merged',required=False,
                              help="Merged reads from flash or fastp")
 
-    parser_asm.add_argument('--careful',required=False, action='store_true',dest='isolate',
-                            help="Run --careful mode not --isolate mode in spades (Default)")
+    parser_asm.add_argument('--careful',required=False, action='store_true',default=True,
+                            help="Run --careful mode in spades (Default)")
+
+    parser_asm.add_argument('--no-careful',required=False, action='store_false',default=True,dest='careful')
 
     parser_asm.add_argument('--isolate',required=False, action='store_true',
                             help="Run --isolate mode not --careful mode in spades")
-    parser.set_defaults(isolate=False)
 
     parser_asm.add_argument('-v','--debug',action='store_true',
                              help="Print Spades stdout to terminal")

diff --git a/AAFTF/assemble.py b/AAFTF/assemble.py
@@ -14,9 +14,14 @@ def run_spades(parser,args):
     if not args.workdir:
         args.workdir = 'spades_'+str(uuid.uuid4())[:8]
 
-    runcmd = ['spades.py','--threads', str(args.cpus), '--mem', args.memory, '--careful',
+    runcmd = ['spades.py','--threads', str(args.cpus), '--mem', args.memory,
               '-o',args.workdir]
 
+    if args.isolate:
+        runcmd.extend(['--isolate'])
+    elif args.careful:
+        runcmd.extend(['--careful'])
+
     if args.assembler_args:
         runcmd.extend(args.assembler_args)