The sample config should be in [__JSON__](http://www.json.org/)format
The sample config should be in [__JSON__](http://www.json.org/)or [__YAML__](http://yaml.org/) format. For yaml the file should be named *.yml or *.yaml.
- First field should have the key __"samples"__
- Second field should contain the __"libraries"__
...
...
@@ -10,7 +10,21 @@ The sample config should be in [__JSON__](http://www.json.org/) format
- The fastq input files can be provided zipped and un zipped
#### Example sample config
~~~
###### yaml:
``` yaml
samples:
Sample_ID1:
libraries:
MySeries_1:
R1:R1.fastq.gz
R2:R2.fastq.gz
```
###### json:
``` json
{
"samples":{
"Sample_ID1":{
...
...
@@ -23,26 +37,19 @@ The sample config should be in [__JSON__](http://www.json.org/) format
}
}
}
~~~
```
-For BAM files as input one should use a config like this:
For BAM files as input one should use a config like this:
~~~
{
"samples":{
"Sample_ID_1":{
"libraries":{
"Lib_ID_1":{
"bam":"MyFirst.bam"
},
"Lib_ID_2":{
"bam":"MySecond.bam"
}
}
}
}
}
~~~
``` yaml
samples:
Sample_ID_1:
libraries:
Lib_ID_1:
bam:MyFirst.bam
Lib_ID_2:
bam:MySecond.bam
```
Note that there is a tool called [SamplesTsvToJson](../tools/SamplesTsvToJson.md) this enables a user to get the sample config without any chance of creating a wrongly formatted JSON file.
