BD2KGenomics / toil-scripts

Toil workflows for common genomic pipelines

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Run real-world pipeline with cwltoil on a multi-node Mesos cluster #55

Open jvivian opened 9 years ago

jvivian commented 9 years ago

When Kyle finishes the MC3 variant pipeline, we can try running it on Toil via CWL.

hannes-ucsc commented 8 years ago

@benedictpaten, @jvivian, is this still a thing?

hannes-ucsc commented 8 years ago

The pupose of the ticket is to validated CWL support for Toil. Since MC3 status is unknown, @jvivian to ask @tetron for a alternative CWL-based workflow.

tetron commented 8 years ago

I have a variant calling pipeline from bcbio-nextgen. I tried running it previously but was blocked by #816. I see that is now resolved so I'll try again.

jvivian commented 8 years ago

Cool, thanks @tetron — if it's successful let me know!

hannes-ucsc commented 8 years ago

@tetron, please reassign to @jvivian once you validated your bcbio-nextgen pipeline.

tetron commented 8 years ago

@hannes-ucsc So now I'm running into a new problem: https://github.com/BD2KGenomics/toil/issues/859

hannes-ucsc commented 8 years ago

859 is fixed. How do we move forward with this? Pinging @chapmanb.