Commit cf14af6f authored by Claire Kuchly's avatar Claire Kuchly
Browse files

ONT nG6 pipeline debut

parent 65705fb8
#
# 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 logging
from ng6.ng6workflow import NG6Workflow
from ng6.utils import Utils
class OntQualityCheck (NG6Workflow):
def get_name(self):
return 'ont_qc'
def get_description(self):
return "ONT data loading and quality check"
def define_parameters(self, function="process"):
logging.getLogger("jflow").debug("Begin OntQualityCheck.define_parameters! ont_qc")
self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "none")
#self.add_parameter("nb_threads", "Number of threads to use for fastqc. Each thread will be allocated 250MB of memory.", default=3)
#self.add_parameter("min_subreads_length", "Subreads shorter than this value (in base pairs) are filtered out and excluded from analysis", default=0, type='int')
#self.add_parameter("polymerase_read_qual", "Polymerase reads with lower quality than this value are filtered out and excluded from analysis", default=0, type='float')
#self.add_parameter("polymerase_read_length", "Polymerase reads shorter than this value (in base pairs) are filtered out and excluded from analysis", default=0, type='int')
#self.add_parameter("barcode_score", "Min identical base for barcode", default=22, type='int')
self.add_input_file( "summary_file", "Input summary basecalling file", default=None)
def process(self):
logging.getLogger("jflow").debug("Begin OntQualityCheck.process! test ont_qc")
sample_names = []
infiles = []
for sample in self.samples :
sample_names.append( sample.name )
infiles.append(sample.reads1[0])
# add raw
addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.get_all_reads(), self.compression])
#add_ont_raw_file = self.add_component("AddOntRawFiles", [self.runobj, self.get_all_reads()])
#h5tofastq = self.add_component("H5toFastq", [sample_names, infiles])
#fastqc = self.add_component("FastQC", [h5tofastq.output_fastqs, False, False, "fastqc.tar.gz", self.nb_threads], parent = h5tofastq)
#self.add_component("RS_Subreads", [sample_names, infiles,self.min_subreads_length,self.polymerase_read_qual,self.polymerase_read_length,self.barcode_file,self.barcode_score ])
#
# 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/>.
#
--date
31/07/2017
--data-nature
DNA
--sequencer
ONT_MinION
--name
ont_qc
--type
Unknown
--species
arabido
--description
ont demo workflow
--project-name
test-dev
--sample
sample-name=ONT_sample
read1=/MinION/20170308_arab1D_LSK108_MN19767/20170308_arab1D_LSK108_MN19767_albacorev1.2.4/20170308_arab1D_LSK108_MN19767_albacorev1.2.4.fastq
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