Commit 08e4b344 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added yaml

parent dcd106b2
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
### The sample config ### The sample config
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"__ - First field should have the key __"samples"__
- Second field should contain the __"libraries"__ - Second field should contain the __"libraries"__
...@@ -10,7 +10,21 @@ The sample config should be in [__JSON__](http://www.json.org/) format ...@@ -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 - The fastq input files can be provided zipped and un zipped
#### Example sample config #### Example sample config
~~~
###### yaml:
``` yaml
samples:
Sample_ID1:
libraries:
MySeries_1:
R1: R1.fastq.gz
R2: R2.fastq.gz
```
###### json:
``` json
{ {
"samples":{ "samples":{
"Sample_ID1":{ "Sample_ID1":{
...@@ -23,26 +37,19 @@ The sample config should be in [__JSON__](http://www.json.org/) format ...@@ -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:
~~~ ``` yaml
{ samples:
"samples":{ Sample_ID_1:
"Sample_ID_1":{ libraries:
"libraries":{ Lib_ID_1:
"Lib_ID_1":{ bam: MyFirst.bam
"bam":"MyFirst.bam" Lib_ID_2:
}, bam: MySecond.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. 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.
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