Run_Demultiplex_Reads.sh

# This file is part of nit_picker.
#
# nit_picker is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# nit_picker 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with nit_picker. If not, see <http://www.gnu.org/licenses/>.


# TODO change these to relative paths. Probably easy.

source /home/ben/minionvenv/bin/activate

#ReadDirectory="/home/ben/ben_share/2017.Nov10.DQA.1d2/raw"
#ResultsOutputDirectory="/home/ben/ben_share/2017.Nov10.DQA.1d2/demultiplex_nitpicker"
#ReferenceFile="/home/ben/Github/nanopore_prospector/33332_analyze_read_quality/HLA_Reference_33332_A24.fasta"
#BarcodeFile="/home/ben/Github/nanopore_prospector/barcodes/barcodes_96_bc_kit.txt"

#python nit_picker_main.py \
# --reads=$ReadDirectory \
# --outputdir=$ResultsOutputDirectory \
# --reference=$ReferenceFile \
# --barcode=$BarcodeFile \