| Topic: | MIT BIG meeting: bcbio and CWL (http://openwetware.org/wiki/BioMicroCenter:BIG_meeting) |
| Time: | Nov 2, 2017 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/223311944 |
| Telephone: | US: +1 646 876 9923 or +1 669 900 6833 or +1 408 638 0968 or international https://zoom.us/zoomconference?m=qoCDInqg9wlWdANSN9knRp5E41dRbRhy |
| Meeting ID: | 223 311 944 |
| Recording: | https://youtu.be/nJEDS9Qol8M |
| Slides: | https://github.com/chapmanb/bcbb/blob/master/talks/big2017_bcbio_cwl/big2017_bcbio_cwl.pdf |
Blue Collar Bioinformatics (bcbio; http://bcb.io/) is community developed methods for variant calling, RNA-seq, small RNA and ChiP-seq 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 provide a followup on our proposals last year to move bcbio to use Common Workflow Language (CWL; http://www.commonwl.org/) for describing workflows. We run full workflows across multiple environments using CWL and will discuss:
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How CWL and the Workflow Definition Language (WDL; http://openwdl.org/) compare to workflow runners (Snakemake, Nextflow, Galaxy...).
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How standard workflow definitions improve community interoperability.
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Examples of supported CWL workflows in bcbio: somatic tumor/normal and germline joint calling with GATK4 and strelka (https://github.com/bcbio/bcbio_validation_workflows); and in progress work: structural variant calling and RNA-seq analysis. We're actively integrating these into a continuous integration environment as part of the GA4GH DREAM execution challenge (https://www.synapse.org/#!Synapse:syn8507133/wiki/415976).
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Practical examples of running bcbio in multiple locations using CWL (https://bcbio-nextgen.readthedocs.io/en/latest/contents/cwl.html):
- Single machine multicore using Rabix Bunny (https://github.com/rabix/bunny)
- HPC schedulers using Toil (http://toil.readthedocs.io/en/latest/)
- DNAnexus (https://github.com/dnanexus/dx-cwl)
- Arvados (https://arvados.org/)
- Seven Bridges (http://docs.sevenbridges.com/docs/sdk-overview)
We support bcbio CWL development at the Harvard Chan Bioinformatics core (http://bioinformatics.sph.harvard.edu/) through collaborations with AstraZeneca Oncology (https://www.astrazeneca.com/our-focus-areas/oncology.html), AstraZeneca Centre for Genomics Research (https://www.astrazeneca.com/Harnessing-the-code-of-life-to-develop-new-treatments.html), The University of Melbourne Centre for Cancer Research (https://www.victorianccc.org.au/) and Veritas (https://www.veritasgenetics.com/).
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 and we'll record the talk and make it available.
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