#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def bowtie(sample, bowtie_flag):
'''Runs Bowtie to align .fastq files.
input:
.fastq file
output:
sample.bam
citation:
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25
link:
http://bowtie-bio.sourceforge.net/index.shtml
parameters from parameters file:
ENDS:
TRIMMED_DATA_PATH:
BOWTIE_OPTIONS:
BOWTIE_INDEX:
BOWTIE_RESULTS:
BOWTIE_VERSION:
SAMTOOLS_VERSION:
BEDTOOLS_VERSION:
TEMP_DIR:
'''
spawn_job(jobname = 'bowtie', 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 = "15gb", script = "/bowtie_drmaa_" + p.ENDS + ".sh", args_list = [sample,p.TRIMMED_DATA_PATH,p.BOWTIE_OPTIONS, p.BOWTIE_INDEX, p.BOWTIE_RESULTS, p.BOWTIE_VERSION, p.SAMTOOLS_VERSION, p.BEDTOOLS_VERSION, p.TEMP_DIR])
job_status(jobname = 'bowtie', resultspath = p.BOWTIE_RESULTS, SAMPLE = sample, outputfilename = sample + "/" + sample + ".bam", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
bowtie(sample, bowtie_flag)
sys.exit(0)