From 67d911cd8f1d8c4c6721063111f3b141176572ee Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 28 Jul 2015 10:13:41 +0200
Subject: [PATCH] Adding minimal config
---
docs/pipelines/mapping.md | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/docs/pipelines/mapping.md b/docs/pipelines/mapping.md
index 5fae9a6a6..b383dab41 100644
--- a/docs/pipelines/mapping.md
+++ b/docs/pipelines/mapping.md
@@ -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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