Commit b4dbc08a authored by Peter van 't Hof's avatar Peter van 't Hof

Update docs

parent 74b4b36b
......@@ -13,6 +13,7 @@ After the QC, the pipeline simply maps the reads with the chosen aligner. The re
* <a href="http://bio-bwa.sourceforge.net/bwa.shtml" target="_blank">Bwa mem</a>
* <a href="http://bio-bwa.sourceforge.net/bwa.shtml" target="_blank">Bwa aln</a>
* <a href="http://bowtie-bio.sourceforge.net/index.shtml" target="_blank">Bowtie version 1.1.1</a>
* <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" target="_blank">Bowtie version 2.*</a>
* <a href="http://www.well.ox.ac.uk/project-stampy" target="_blank">Stampy</a>
* <a href="http://research-pub.gene.com/gmap/" target="_blank">Gsnap</a>
* <a href="https://ccb.jhu.edu/software/tophat" target="_blank">TopHat</a>
......@@ -114,15 +115,15 @@ Any supplied sample config will be ignored.
#### Minimal
```json
{
"reference_fasta": "<path/to/reference">,
"output_dir": "<path/to/output/dir">
"reference_fasta": "<path/to/reference>",
"output_dir": "<path/to/output/dir>"
}
```
#### With options
```json
{
"reference_fasta": "<path/to/reference">,
"reference_fasta": "<path/to/reference>",
"aligner": "bwa",
"skip_metrics": true,
"platform": "our_platform",
......
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