Commit c0f2136e authored by Penom Nom's avatar Penom Nom
Browse files

pacbio quality check pipeline

parent fd41415b
#
# 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
from ng6.ng6workflow import NG6Workflow
from ng6.utils import Utils
class PacBioQualityCheck (NG6Workflow):
def get_name(self):
return 'pacbio_qc'
def get_description(self):
return "PacBio quality check pipeline"
def define_parameters(self, function="process"):
self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "none")
def process(self):
addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.get_all_reads(), self.compression])
fastqc = self.add_component("FastQC", [self.get_all_reads(), False, False, "fastqc.tar.gz"])
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