Commit 67d911cd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding minimal config

parent b0289eef
......@@ -10,9 +10,12 @@ After the QC, the pipeline simply maps the reads with the chosen aligner. The re
* [Flexiprep](flexiprep.md)
* Alignment programs:
* <a href="http://bio-bwa.sourceforge.net/bwa.shtml" target="_blank">BWA</a>
* <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://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>
* <a href="https://github.com/alexdobin/STAR" target="_blank">Star</a>
* <a href="https://github.com/alexdobin/STAR" target="_blank">Star-2pass</a>
* <a href="http://broadinstitute.github.io/picard/" target="_blank">Picard tool suite</a>
......@@ -58,6 +61,16 @@ Note that one should first create the appropriate [settings config](../general/c
Any supplied sample config will be ignored.
### Example config
#### Minimal
```json
{
"reference_fasta": "<path/to/reference">,
"output_dir": "<path/to/output/dir">
}
```
#### With options
```json
{
"reference_fasta": "<path/to/reference">,
......@@ -109,5 +122,6 @@ To perform a dry run simply remove `-run` from the commandline call.
   ├── <samplename>-lib_1.dedup.bam
   ├── <samplename>-lib_1.dedup.metrics
   ├── flexiprep
└── metrics
├── metrics
└── report
~~~
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