Commit 609396ba authored by ckuchly's avatar ckuchly
Browse files

Add Illumina_10X workflow

parent 62e909d6
#
# Copyright (C) 2012 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import os
import sys
import re
import logging
from ng6.ng6workflow import CasavaNG6Workflow
from ng6.utils import Utils
class Illumina10XQualityCheck (CasavaNG6Workflow):
def get_name(self):
return 'illumina_10X_qc'
def get_description(self):
return "illumina quality check pipeline for 10X analyses"
def define_parameters(self, function="process"):
self.add_input_file("reference_genome", "Which genome should the read being align on")
def process(self):
fastqilluminafilter, filtered_read1_files, filtered_read2_files, concat_files = self.illumina_process()
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