From 17d24305d0425f21b2abd686420e0e1ed41f62df Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Mon, 13 Apr 2020 20:13:40 -0400 Subject: [PATCH] pass threads as int to fastqc --- reports.py | 2 +- tools/fastqc.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/reports.py b/reports.py index 95946a53..ae4b2c4a 100755 --- 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 index 4f98f528..41b94553 100644 --- 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