From 51f89832389386b87b3e2be7e3072b72d905538d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 27 Aug 2018 11:21:52 +0200
Subject: [PATCH] peak_calling_single.nf: select lp0 autoamtically
---
src/nf_modules/MUSIC/peak_calling_single.nf | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/src/nf_modules/MUSIC/peak_calling_single.nf b/src/nf_modules/MUSIC/peak_calling_single.nf
index 3a29726c..da16eb95 100644
--- a/src/nf_modules/MUSIC/peak_calling_single.nf
+++ b/src/nf_modules/MUSIC/peak_calling_single.nf
@@ -1,8 +1,8 @@
params.reads_size = 100
params.frag_size = 200
-params.begin_l = 50
-params.end_l = 500
-
+params.step_l = 50
+params.min_l = 200
+params.max_l = 5000
log.info "bam files : ${params.bam}"
log.info "index files : ${params.index}"
log.info "fasta files : ${params.fasta}"
@@ -94,11 +94,10 @@ tar -xf ${control} -C control/
tar -xf ${chip} -C chip/
MUSIC -get_per_win_p_vals_vs_FC -chip chip/ -control control/ \
- -l_win_step ${params.end_l} \
- -l_win_min ${params.end_l} -l_win_max ${params.end_l * 10}
+ -l_win_step ${params.step_l} \
+ -l_win_min ${params.min_l} -l_win_max ${params.max_l}
MUSIC -get_multiscale_punctate_ERs \
-chip chip/ -control control/ -mapp mappability/ \
- -begin_l ${params.begin_l} -end_l ${params.end_l} -step 1.1 \
-l_mapp ${params.reads_size} -l_frag ${params.frag_size} -q_val 1 -l_p 0
ls -l
"""
--
GitLab