#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def cutadapt_miRNA(sample, cutadapt_miRNA_flag):
'''Runs Cutadapt to trim adapters from reads.
input:
.fastq
output:
.fastq
citation:
Martin 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10-12.
link:
https://code.google.com/p/cutadapt/
parameters from parameters file:
RAW_DATA_DIR:
ADAPTER:
TRIMMED_DATA_PATH:
PYTHON_VERSION'''
spawn_job(jobname = 'cutadapt_miRNA', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "120:00:00", queue = p.QUEUE, nodes = 1, ppn = 8, memory = "15gb", script = "/cutadapt_drmaa.sh", args_list = [sample, p.RAW_DATA_DIR, p.ADAPTER, p.TRIMMED_DATA_PATH, p.PYTHON_VERSION])
job_status(jobname = 'cutadapt_miRNA', resultspath = p.TRIMMED_DATA_PATH, SAMPLE = sample, outputfilename = sample + "_trimmed.fastq", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
cutadapt_miRNA(sample, cutadapt_miRNA_flag)
sys.exit(0)