Commit b0289eef authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed link

parent 761cb9f5
......@@ -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
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......@@ -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
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