This mean can extract samples, libraries and readgroups from a sample config file. This meant as a supporting tool inside wdl pipelines. It can also output a single layer as tsv file.


SampleConfig requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.

Download the latest version of SampleConfig here. To generate the usage run:

java -jar <SampleConfig_jar> --help


This tool can support multiple sample config files, this files will be merged into 1 large config. Depending if sample/library if given the list is given, see also the examples


Extracting samples, list goes to stdout:

java -jar <SampleConfig_jar> \
-i <input config>

Extracting libraries, list go to stdout:

java -jar <SampleConfig_jar> \
-i <input config> \
--sample <sample name>

Extracting readgroups, list go to stdout:

java -jar <SampleConfig_jar> \
-i <input config> \
--sample <sample name> \
--library <library name>


Usage for SampleConfig:

Option Required Can occur multiple times Description
--log_level, -l no no Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
--help, -h no no Print usage
--version, -v no no Print version
--inputFile, -i yes yes (unlimited) Input sample json, can give multiple file
--sample no no Sample name
--library no no Library Name
--readgroup no no Readgroup name
--jsonOutput no no json output file
--tsvOutput no no tsv output file


SampleConfig is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.


The source code of SampleConfig can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

SampleConfig is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on SampleConfig. We have had good results with this IDE.


For any question related to SampleConfig, please use the github issue tracker or contact the SASC team directly at: