This repository contains a collection of BioWDL workflows which can be used for aligning sequencing data. There is currently one workflow available:
- align-star.wdl: Uses STAR to align RNA.
- align-hisat2.wdl: Uses HISAT2 to align RNA.
These workflows are part of BioWDL developed by the SASC team at Leiden University Medical Center.
Dependency requirements and tool versions
Biowdl pipelines use docker images to ensure reproducibility. This means that biowdl pipelines will run on any system that has docker installed. Alternatively they can be run with singularity.
For more advanced configuration of docker or singularity please check the cromwell documentation on containers.
Images from biocontainers are preferred for
biowdl pipelines. The list of default images for this pipeline can be
found in the default for the dockerImages input.
Contact
For any questions about running these workflows and feature request (such as adding additional options), please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.