adding toucan to docs

docs/pipelines/toucan.md

+TOUCAN
+===========
+
+Introduction
+-----------
+The Toucan pipeline is a VEP-based annotation pipeline. 
+Currently, it comprises just two steps:
+
+* Variant Effect Predictor run
+* [VEP Normalizer on the VEP output](../tools/VEPNormalizer.md)
+
+Example
+-----------
+~~~~bash
+java -jar Biopet-0.3.0.jar pipeline Toucan -h
+Arguments for Toucan:
+ -Input,--inputvcf <inputvcf>          Input VCF file
+ -config,--config_file <config_file>   JSON config file(s)
+ -DSC,--disablescatter                 Disable all scatters
+~~~~
+
+Configuration
+-------------
+You can set all the usual [flags and options](http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html) of the VEP in the configuration,
+with the same name used by native VEP.
+As some of these flags might conflict with other Biopet tools/pipelines, it is wise to put the VEP in its own JSON object.
+
+You **MUST** set the following fields:
+
+* `vep_script`: the path to the VEP executable
+* `dir` or `dir_cache`: the path to the VEP cache
+
+It is wise to set the `cache_version` field as well.
+Furthermore, the `fork` field will be overwritten by `threads` in case that one exists in the config. 
+Therefore, it is recommended not to use `fork`, but to rather use `threads`. 
+
+With that in mind, an example configuration using mode `standard` of the VEPNormalizer would thus be:
+~~~~
+{
+    "varianteffectpredictor": {
+        "vep_script": <path_to_exe>,
+        "dir": <path_to_cache>,
+        "cache_version": <cache_version>,
+        "threads": 8 
+    },
+    "vepnormalizer": {
+        "mode": "standard"
+    },
+    "out_dir": <path_to_output_directory>
+}
+~~~~
+
+Running the pipeline
+---------------
+The command to run the pipeline is:
+~~~~
+java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run
+~~~~
+
+If one wishes to run it on a cluster, the command becomes
+~~~~
+java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run -qsub -jobParaEnv <PE>
+~~~~

mkdocs.yml

@@ -7,6 +7,7 @@ pages:
 - ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
 - ['pipelines/mapping.md', 'Pipelines', 'Mapping']
 - ['pipelines/sage.md', 'Pipelines', 'Sage']
+- ['pipelines/toucan.md', 'Pipelines', 'Toucan']
 - ['tools/SamplesTsvToJson.md','Tools','SamplesTsvToJson']
 - ['tools/BastyGenerateFasta.md','Tools','BastyGenerateFasta']
 - ['tools/bedtointerval.md','Tools','BedToInterval']