Changes in docs

docs/config.md

@@ -9,6 +9,7 @@ The sample config should be in [__JSON__](http://www.json.org/) format
 - Third field contains __"R1" or "R2"__ or __"bam"__
 - The fastq input files can be provided zipped and un zipped
 
+#### Example sample config
 ~~~
     {  
        "samples":{  
@@ -48,4 +49,50 @@ Note that there is a tool called [SamplesTsvToJson](tools/SamplesTsvToJson.md) t
 
 
 ### The settings config
-The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
+The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
\ No newline at end of file
+This config file should be written in JSON format. It can contain setup settings like references for the tools used,
+if the pipeline should use chunking or setting memory limits for certain programs almost everything can be adjusted trough this config file.
+One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer deeper into the JSON file.
+E.g. in the example below the settings for Picard tools are altered only for Picard and not global. 
+
+~~~
+"picard": { "validationstringency": "LENIENT" } 
+~~~
+
+Global setting examples are:
+~~~
+"java_gc_timelimit": 98,
+"numberchunks": 25,
+"chunking": true
+~~~
+
+
+----
+
+#### 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",
+        "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",
+        "min_dp": 5,
+        "bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
+        "bam_to_fastq": true,
+        "baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
+        "samtofastq": {"memory_limit": 8, "vmem": "16G"},
+        "java_gc_timelimit": 98,
+        "numberchunks": 25,
+        "chunking": true,
+        "haplotypecaller": { "scattercount": 1000 }
+}
+~~~
+
+### 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

docs/pipelines/basty.md

 # Introduction
 
+## [Basty](https://git.lumc.nl/biopet/biopet/tree/develop/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty)
+
+A pipeline for aligning bacterial genomes and detect structural variations on the level of SNPs. Basty will output phylogenetic trees.
+Which makes it very easy to look at the variations between certain species.
+
+# Tools
+* GATK-pipeline []()
+* FASTA builder [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
+* RAxml []()
+* Gubbins []()
+
 # Invocation
 
 # Example

docs/pipelines/flexiprep.md

 # Introduction
 
-# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/master/flexiprep)
+# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/develop/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep)
 
 QC pipeline for fastq files
 

mkdocs.yml

@@ -2,13 +2,14 @@ site_name: Biopet user manual
 pages:
 - ['index.md', 'Home']
 - ['config.md', 'Config']
-- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
 - ['pipelines/basty.md', 'Pipelines', 'Basty']
 - ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
 - ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
 - ['pipelines/mapping.md', 'Pipelines', 'Mapping']
 - ['pipelines/sage.md', 'Pipelines', 'Sage']
 - ['pipelines/yamsvp.md', 'Pipelines', 'Yamsvp']
+- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
+- ['tools/BastyGenerateFasta.md','tools','BastyGenerateFasta']
 - ['cluster/oge.md', 'OpenGridEngine']
 - ['about.md', 'About']
 - ['license.md', 'License']