diff --git a/docs/config.md b/docs/config.md index c10419859bed6d3f510c80afe0b27fea913d774f..de3342b195b1dc7acb338729792d9dabc59c5228 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.