Blue Collar Bioinformatics (bcbio; http://bcb.io/) is community developed methods for variant calling, RNA-seq, small RNA and other biological analyses. We work together to build openly available, practical, validated tools for working with high throughput sequencing data.
At the MIT BIG meeting I'll discuss ongoing work to replace the infrastructure components of bcbio with the Common Workflow Language (CWL http://www.commonwl.org/). This allows integration of bcbio developed pipelines with multiple open source and commercial products. The goal is to improve how projects work together, giving bcbio users multiple infrastructure and hardware options including local HPC and multiple cloud vendors like AWS, Google Cloud and Microsoft Azure. Our ongoing work includes integration with these platforms:
- Arvados (https://arvados.org/)
- Toil (http://toil.readthedocs.io/en/latest/)
- Cromwell via conversion to WDL (http://gatkforums.broadinstitute.org/wdl/discussion/8454/feedback-on-initial-version-of-bcbio-wdl-converted-from-cwl)
- Galaxy (https://f1000research.com/posters/5-2567)
- Nextflow via conversion to their DSL (https://www.nextflow.io/)
- Seven Bridges (http://docs.sevenbridges.com/docs/sdk-overview)
- DNAnexus via conversion to their API (https://www.dnanexus.com/developer-resources)
I'll talk about the ongoing challenges of migrating to CWL and supporting bcbio development at the Harvard Chan Bioinformatics core (http://bioinformatics.sph.harvard.edu/).
You're welcome to attend in person at MIT if you're in the Boston area. The presentation will also be online through Zoom for remote participation.
| Topic: | MIT BIG meeting: bcbio and CWL (http://openwetware.org/wiki/BioMicroCenter:BIG_meeting) |
| Recording: | https://youtu.be/375QSYmaidk |
| Slides: | https://github.com/chapmanb/bcbb/blob/master/talks/big2016_bcbio_cwl/big2016_bcbiocwl.pdf |
| Time: | Nov 3, 2016 11:00 AM (GMT-4:00) Eastern Time (US and Canada) |
| Location: | MIT Koch Biology Building 68-156 (http://whereis.mit.edu/?go=68) or online |
| Online: | https://zoom.us/j/191593233 |
| On Telephone: | +1 646 558 8656 (US Toll) or +1 408 638 0968 (US Toll) International numbers available: https://zoom.us/zoomconference?m=_MZZb0sUZiQx1enkS_HU-S_D15BOJJjo |
| Meeting ID: | 191 593 233 |