From 7e7e25265b7cddbe03b1c943acca5b618b9c3efa Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Wed, 17 Dec 2014 15:02:49 +0100
Subject: [PATCH] remove dirstructure from config
---
docs/config.md | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/docs/config.md b/docs/config.md
index c10419859..de3342b19 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -72,16 +72,16 @@ Global setting examples are:
#### Example settings config
~~~
{
- "reference": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/ucsc.hg19_nohap.fasta",
- "dbsnp": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
+ "reference": "/references/hg19_nohap/ucsc.hg19_nohap.fasta",
+ "dbsnp": "/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
"joint_variantcalling": false,
"haplotypecaller": { "scattercount": 100 },
"multisample": { "haplotypecaller": { "scattercount": 1000 } },
"picard": { "validationstringency": "LENIENT" },
"library_variantcalling_temp": true,
- "target_bed_temp": "/data/LGTC/projects/vandoorn-melanoma/analysis/target.bed",
+ "target_bed_temp": "analysis/target.bed",
"min_dp": 5,
- "bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
+ "bedtools": {"exe":"/BEDtools/bedtools-2.17.0/bin/bedtools"},
"bam_to_fastq": true,
"baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
"samtofastq": {"memory_limit": 8, "vmem": "16G"},
@@ -95,4 +95,4 @@ Global setting examples are:
### JSON validation
To check if the JSON file created is correct we can use multiple options the simplest way is using [this](http://jsonformatter.curiousconcept.com/)
-website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
\ No newline at end of file
+website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
--
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