From dfed27c23d44f50ec883d42fe450f9b1a8280f19 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 20 Sep 2017 14:09:12 -0500
Subject: [PATCH] update syntax and order of qc_fastq.py
---
workflow/scripts/qc_fastq.py | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/workflow/scripts/qc_fastq.py b/workflow/scripts/qc_fastq.py
index f58cb9f..991d927 100755
--- a/workflow/scripts/qc_fastq.py
+++ b/workflow/scripts/qc_fastq.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python3
-# -*- coding: latin-1 -*-
+
'''QC check of raw .fastq files using FASTQC.'''
import os
@@ -23,19 +23,6 @@ LOGGER.propagate = False
LOGGER.setLevel(logging.INFO)
-def check_tools():
- '''Checks for required componenets on user system'''
-
- LOGGER.info('Checking for required libraries and components on this system')
-
- fastqc_path = shutil.which("fastqc")
- if fastqc_path:
- LOGGER.info('Found fastqc: %s', fastqc_path)
- else:
- print("Please install 'fastqc' before using the tool")
- sys.exit()
-
-
def get_args():
'''Define arguments.'''
parser = argparse.ArgumentParser(
@@ -51,6 +38,19 @@ def get_args():
return args
+def check_tools():
+ '''Checks for required componenets on user system'''
+
+ LOGGER.info('Checking for required libraries and components on this system')
+
+ fastqc_path = shutil.which("fastqc")
+ if fastqc_path:
+ LOGGER.info('Found fastqc: %s', fastqc_path)
+ else:
+ print("Please install 'fastqc' before using the tool")
+ sys.exit()
+
+
def check_qual_fastq(fastq):
'''Run fastqc on 1 or 2 files.'''
qc_command = "fastqc -t -f fastq " + " ".join(fastq)
--
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