From 9cd23b43821be4fea8194938298248115f5cbc05 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Fri, 16 Feb 2018 22:19:36 +0100
Subject: [PATCH] New parameters for simulations
---
Snake.config.json | 8 ++++----
Snakefile | 8 ++++----
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index f0a8d93..abae56b 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -21,8 +21,8 @@
"bp_density" : {
"few" : 0.1,
- "medium" : 0.33,
- "many" : 0.9
+ "medium" : 0.25,
+ "many" : 0.5
},
"paired_end" : false,
@@ -34,10 +34,10 @@
"100000" : 0.3,
"500000" : 0.1,
},
- "simulation_min_reads_per_library" : 250000,
+ "simulation_min_reads_per_library" : 500000,
"simulation_max_reads_per_library" : 1000000,
"simulation_window_sizes" : [50000, 100000],
- "simulation_cell_count" : 200,
+ "simulation_cell_count" : 100,
"simulation_alpha" : 0.02,
"genome_size" : 3e9
diff --git a/Snakefile b/Snakefile
index 8b357e9..450db68 100644
--- a/Snakefile
+++ b/Snakefile
@@ -45,10 +45,10 @@ rule simulate_genome:
log:
"log/simulate_genome/genome{seed}.tsv"
params:
- svcount=200,
- minsize=1000,
- maxsize=2000000,
- mindistance=1000000,
+ svcount = 200,
+ minsize = 100000,
+ maxsize = 5000000,
+ mindistance = 1000000,
shell:
"utils/simulate_SVs.R {wildcards.seed} {params.svcount} {params.minsize} {params.maxsize} {params.mindistance} {output.tsv} > {log} 2>&1"
--
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