#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def fastqc(sample, fastqc_flag):
'''QC check of raw .fastq files using FASTQC.
input:
.fastq file
output:
folder and zipped folder containing html, txt and image files
citation:
Babraham Bioinformatics
link:
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
parameters from parameters file:
RAW_DATA_DIR:
QC_PATH:
FASTQC_VERSION:
COMPRESSION:
'''
print "sample name is: ", sample
if p.ENDS == "PE":
SAMPLE1 = sample + "_1"
SAMPLE2 = sample + "_2"
spawn_job(jobname = 'fastqc', SAMPLE = SAMPLE1, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "12:00:00", queue = p.QUEUE, nodes = 1, ppn = 1, memory = "4gb", script = "/fastqc_drmaa.sh", args_list = [SAMPLE1, p.RAW_DATA_DIR,p.QC_PATH, p.FASTQC_VERSION, p.COMPRESSION])
spawn_job(jobname = 'fastqc', SAMPLE = SAMPLE2, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "12:00:00", queue = p.QUEUE, nodes = 1, ppn = 1, memory = "4gb", script = "/fastqc_drmaa.sh", args_list = [SAMPLE2, p.RAW_DATA_DIR,p.QC_PATH, p.FASTQC_VERSION, p.COMPRESSION])
job_status(jobname = 'fastqc', resultspath = p.QC_PATH, SAMPLE = sample, outputfilename = SAMPLE1 +"/" + SAMPLE1 + "_fastqc.html", FLAG_PATH = p.FLAG_PATH)
else:
spawn_job(jobname = 'fastqc', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "12:00:00", queue = p.QUEUE, nodes = 1, ppn = 1, memory = "4gb", script = "/fastqc_drmaa.sh", args_list = [sample, p.RAW_DATA_DIR,p.QC_PATH, p.FASTQC_VERSION, p.COMPRESSION])
job_status(jobname = 'fastqc', resultspath = p.QC_PATH, SAMPLE = sample, outputfilename = sample +"/" + sample + "_fastqc.html", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
fastqc(sample, fastqc_flag)
sys.exit(0)