#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def picard_mark_duplicates(sample, picard_mark_duplicates_flag):
'''Picard tools Mark Duplicates.
input:
sorted.bam
output:
_sorted.rg.md.bam
citation:
http://picard.sourceforge.net/
link:
http://picard.sourceforge.net/
parameters from parameters file:
BWA_RESULTS:
TEMP_DIR:
PICARD_VERSION:
SAMTOOLS_VERSION:
'''
spawn_job(jobname = 'picard_mark_duplicates', 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 = 8, memory = "29gb", script = "/picard_mark_duplicates.sh", args_list = [p.BWA_RESULTS, sample, p.TEMP_DIR, p.PICARD_VERSION, p.SAMTOOLS_VERSION])
job_status(jobname = 'picard_mark_duplicates', resultspath = p.BWA_RESULTS, SAMPLE = sample, outputfilename = sample + "/" + sample + "_sorted.rg.md.bam", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
picard_mark_duplicates(sample, picard_mark_duplicates_flag)
sys.exit(0)