Commit 0412afdc authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

add fragment size metrics for paired data

parent 5f620a7b
#########################################################################
# ChIPflow: Standardize and reproducible ChIP-seq analysis from raw #
# data to differential analysis #
# Authors: Rachel Legendre, Maelle Daunesse #
# Copyright (c) 2019-2020 Institut Pasteur (Paris) and CNRS. #
# #
# This file is part of ChIPflow workflow. #
# #
# ChIPflow 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. #
# #
# ChIPflow 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 ChIPflow (LICENSE). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
rule insert_size_metrics :
input :
insert_size_metrics_input
output :
txt = insert_size_metrics_output_txt,
pdf = insert_size_metrics_histo
singularity:
"chipflow.img"
log :
out = insert_size_metrics_log_out,
err = insert_size_metrics_log_err
params :
shell :
"""
PicardCommandLine CollectInsertSizeMetrics I={input} O={output.txt} H={output.pdf} > {log.out} 2> {log.err}
"""
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