diff --git a/workflow/rules/seacr_noCTL.rules b/workflow/rules/seacr_noCTL.rules new file mode 100755 index 0000000000000000000000000000000000000000..e1c75af2d199444c106b36a2db2d72b94e00ab6a --- /dev/null +++ b/workflow/rules/seacr_noCTL.rules @@ -0,0 +1,44 @@ +######################################################################### +# ePeak: 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 ePeak workflow. # +# # +# ePeak 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. # +# # +# ePeak 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 ePeak (LICENSE). # +# If not, see <https://www.gnu.org/licenses/>. # +######################################################################### + + + +rule seacr: + input: + ip = seacr_bed_ip + output: + seacr_output + params: + prefix = seacr_output_prefix, + threshold = seacr_bed_threshold, + norm = seacr_bed_norm + singularity: + "epeak.img" + log: + out = seacr_logs_std, + err = seacr_logs_err + shell: + """ + bash workflow/scripts/SEACR_1.3.sh {input.ip} 0.1 {params.norm} {params.threshold} {params.prefix} > {log.out} 2> {log.err} + + """