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.

To open the help:

java -Xmx2G -jar Biopet-0.2.0.jar tool SamplesTsvToJson -h
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.


  "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