@@ -9,6 +9,7 @@ The sample config should be in [__JSON__](http://www.json.org/) format
- Third field contains __"R1" or "R2"__ or __"bam"__
- The fastq input files can be provided zipped and un zipped
#### Example sample config
~~~
{
"samples":{
...
...
@@ -48,4 +49,50 @@ Note that there is a tool called [SamplesTsvToJson](tools/SamplesTsvToJson.md) t
### The settings config
The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
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The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
This config file should be written in JSON format. It can contain setup settings like references for the tools used,
if the pipeline should use chunking or setting memory limits for certain programs almost everything can be adjusted trough this config file.
One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer deeper into the JSON file.
E.g. in the example below the settings for Picard tools are altered only for Picard and not global.