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This tool enables a user to create a full sample sheet in JSON format suitable for all our Queue pipelines.
The tool can be started as follows:
~~~
java -Xmx2G -jar Biopet-0.2.0.jar tool SamplesTsvToJson
~~~
__-Xmx2G__ defines the amount of memory used to run the tool. Usually one should not change this value since 2G is more than enough.
java -Xmx2G -jar Biopet-0.2.0.jar tool SamplesTsvToJson -h
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Usage: SamplesTsvToJson [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
Print version
-i <file> | --inputFiles <file>
Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed
~~~
The tool is designed in such a way that a user can provide a TAB seperated file (TSV) with sample specific properties and even those will be parsed by the tool.
For example: a user wants to have certain properties e.g. which treatment a sample got than the user should provide a extra columns called treatment and then the
JSON file is parsed with those properties inside it as well. The order of columns does not matter.
#### Example
~~~
{
"samples" : {
"Sample_ID_1" : {
"treatment" : "heatshock",
"libraries" : {
"Lib_ID_1" : {
"bam" : "MyFirst.bam"
}
}
},
"Sample_ID_2" : {
"treatment" : "heatshock",
"libraries" : {
"Lib_ID_2" : {
"bam" : "MySecond.bam"
}
}
}
}
}
~~~
#### Sample definition
To get the above example out of the tool one should provide 2 TSV files as follows:
----
| samples | library | bam |
| ------- | ------- | --------- |
|Sample_ID_1 |Lib_ID_1 |MyFirst.bam |
|Sample_ID_2 |Lib_ID_2 |MySecond.bam |
----
#### Library definition
The second TSV file can contain as much properties as you would like. Possible option would be: gender, age and family.
Basically anything you want to pass to your pipeline is possible.
----
| sample | treatment |
| ----------- | --------- |
| Sample_ID_1 | heatshock |
| Sample_ID_2 | heatshock |