Remove fastqc step.

workflow/scripts/qc_fastq.py

-#!/usr/bin/env python3
-
-'''QC check of raw .fastq files using FASTQC.'''
-
-import os
-import subprocess
-import argparse
-import shutil
-import logging
-import sys
-import json
-
-EPILOG = '''
-For more details:
-        %(prog)s --help
-'''
-
-## SETTINGS
-
-logger = logging.getLogger(__name__)
-logger.addHandler(logging.NullHandler())
-logger.propagate = False
-logger.setLevel(logging.INFO)
-
-
-def get_args():
-    '''Define arguments.'''
-    parser = argparse.ArgumentParser(
-        description=__doc__, epilog=EPILOG,
-        formatter_class=argparse.RawDescriptionHelpFormatter)
-
-    parser.add_argument('-f', '--fastq',
-                        help="The fastq file to run QC check on.",
-                        nargs='+',
-                        required=True)
-
-    args = parser.parse_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:
-        logger.error('Missing fastqc')
-        raise Exception('Missing fastqc')
-
-
-def check_qual_fastq(fastq):
-    '''Run fastqc on 1 or 2 files.'''
-    qc_command = "fastqc -t -f fastq " + " ".join(fastq)
-
-    logger.info("Running fastqc with %s", qc_command)
-
-    qual_fastq = subprocess.Popen(qc_command, shell=True)
-    out, err = qual_fastq.communicate()
-
-
-def main():
-    args = get_args()
-
-    # Create a file handler
-    handler = logging.FileHandler('qc.log')
-    logger.addHandler(handler)
-
-    # Check if tools are present
-    check_tools()
-
-    # Run quality checks
-    check_qual_fastq(args.fastq)
-
-
-if __name__ == '__main__':
-    main()