From 082792f8b27e8962877decf85555b34c8ca7ea23 Mon Sep 17 00:00:00 2001
From: rlegendre <rachel.legendre@pasteur.fr>
Date: Fri, 4 Aug 2023 15:24:17 +0200
Subject: [PATCH] add seacr no control
---
workflow/rules/seacr_noCTL.rules | 44 ++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
create mode 100755 workflow/rules/seacr_noCTL.rules
diff --git a/workflow/rules/seacr_noCTL.rules b/workflow/rules/seacr_noCTL.rules
new file mode 100755
index 0000000..e1c75af
--- /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}
+
+ """
--
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