Fixed link

docs/pipelines/basty.md

@@ -7,7 +7,7 @@ Basty is a pipeline for aligning bacterial genomes and detecting structural vari
 Basty will output phylogenetic trees, which makes it very easy to look at the variations between certain species or strains.
 
 ### Tools for this pipeline
-* [Shiva](../pipelines/shiva.md)
+* [Shiva](shiva.md)
 * [BastyGenerateFasta](../tools/BastyGenerateFasta.md)
 * <a href="http://sco.h-its.org/exelixis/software.html" target="_blank">RAxml</a>
 * <a href="https://github.com/sanger-pathogens/Gubbins" target="_blank">Gubbins</a>
@@ -25,7 +25,7 @@ Each aligner has his own way of creating index files. Therefore the options for
 ### Configuration
 To run Basty, please create the proper [Config](../general/config.md) files.
 
-Batsy uses the [Shiva](../shiva.md) pipeline internally. Please check the documentation for this pipeline for the options.
+Batsy uses the [Shiva](shiva.md) pipeline internally. Please check the documentation for this pipeline for the options.
 
 #### Required configuration values
 

docs/pipelines/shiva.md

@@ -121,7 +121,7 @@ To view all possible config options please navigate to our Gitlab wiki page
 | vcffilter | filter_ref_calls | Boolean | true | Remove reference calls |
 | vcfstats | reference | String | Path to reference to be used by `vcfstats` |
 
-Since Shiva uses the [Mapping](../mapping.md) pipeline internally, mapping config values can be specified as well.
+Since Shiva uses the [Mapping](mapping.md) pipeline internally, mapping config values can be specified as well.
 For all the options, please see the corresponding documentation for the mapping pipeline.
 
 ### Modes