SampleConfig

Tools - ExtractTsv

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.

Tools - ReadFromTsv

This tool enables a user to create a full sample sheet in JSON format or YAML format, suitable for all Biopet Queue pipelines, from TSV file(s).

Tools - CromwellArrays

This tool will convert the sample configs to a array based format that can be used inside wdl pipelines. This tool is only to support biowdl pipelines.

Tools - CaseControl

This tool will extract the case-control pairs from a sample config file. It will read the headers of the bam files to confirm that samples do exist.

Documentation

For documentation and manuals visit our github.io page.

About

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 a pipeline, for example the SASC team’s biowdl pipelines.

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

Contact

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