pass threads as int to fastqc

broadinstitute · Apr 14, 2020 · 17d2430 · 17d2430
1 parent de5c4fb
commit 17d2430
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/reports.py b/reports.py
@@ -1031,7 +1031,7 @@ def parser_fastqc(parser=argparse.ArgumentParser()):
     parser.add_argument('inBam', help='Input reads, BAM format.')
     parser.add_argument('out_html',  help='Output report, HTML format.')
     parser.add_argument('--out_zip', help='Output data, zip archive.')
-    parser.add_argument('--threads', help='Output data, zip archive.')
+    parser.add_argument('--threads', type=int, help='Number of threads.')
     util.cmd.attach_main(parser, tools.fastqc.FastQC().execute, split_args=True)
     return parser
 __commands__.append(('fastqc', parser_fastqc))

diff --git a/tools/fastqc.py b/tools/fastqc.py
@@ -30,7 +30,7 @@ def version(self):
         return TOOL_VERSION
 
     def execute(self, inBam, out_html, out_zip=None, threads=None):    # pylint: disable=W0221
-        threads =  util.misc.sanitize_thread_count(threads=threads)
+        threads =  util.misc.sanitize_thread_count(threads=int(threads))
 
         if tools.samtools.SamtoolsTool().isEmpty(inBam):
             # fastqc can't deal with empty input