Select Git revision
bowtie2_index.rules
bowtie2_index.rules 2.03 KiB
#########################################################################
# RNAflow: an automated pipeline to analyse transcriptomic data #
# #
# Authors: Rachel Legendre #
# Copyright (c) 2021-2022 Institut Pasteur (Paris). #
# #
# This file is part of RNAflow workflow. #
# #
# RNAflow 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. #
# #
# RNAflow 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 RNAflow (LICENSE). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
rule bowtie2_index:
input:
fasta = bowtie2_index_fasta
output:
bowtie2_index_output_done
singularity:
"rnaflow.img"
params:
prefix = bowtie2_index_output_prefix
log:
bowtie2_index_log
envmodules:
"bowtie2",
"samtools"
shell:
"""
bowtie2-build {input.fasta} {params.prefix} 2> {log}
samtools faidx {input.fasta} 2>> {log}
"""