#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def RNAseq_QC(sample, RNAseq_QC_flag):
'''Runs rseqc to determine insert size as QC for alignment.
input:
.bam
output:
pdf plot
link:
http://rseqc.sourceforge.net/
parameters from parameters file:
STAR_RESULTS:
QC_PATH:
BAM_FILE_NAME:
RSEQC_REF:
TEMP_DIR:
PICARD_VERSION:
R_VERSION:
'''
spawn_job(jobname = 'RNAseq_QC', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 1, memory = "12gb", script = "/RNAseq_QC.sh", args_list = [p.STAR_RESULTS, p.QC_PATH, p.BAM_FILE_NAME, p.RSEQC_REF, p.TEMP_DIR, sample, p.PICARD_VERSION, p.R_VERSION])
job_status(jobname = 'RNAseq_QC', resultspath = p.QC_PATH, SAMPLE = sample, outputfilename = sample + "/insertSizeHist.pdf", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
RNAseq_QC(sample, RNAseq_QC_flag)
sys.exit(0)