VC workflows comparison

[thejmazz]

• compare/contrast on workflow systems
• introduction to VC
• identify opportunities for JS (application of streams)

[thejmazz]

https://github.com/codeforscience/pipelines/issues/1

[thejmazz]

Ruffus, Luigi, ratatosk: https://www.biostars.org/p/97766/

[thejmazz]

https://github.com/pharmbio/sciluigi

[thejmazz]

https://www.biostars.org/p/115745/ also https://www.biostars.org/p/91301/ also https://www.biostars.org/p/79/

[thejmazz]

https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems

[thejmazz]

http://www.slideshare.net/ChristianFrech/reproducible-bioinformatics-pipelines-with-docker-and-anduril

[thejmazz]

https://software.broadinstitute.org/wdl/

[thejmazz]

most reputable source: https://www.reddit.com/r/bioinformatics/comments/4jyjwk/your_favorite_workflow_manager/

[thejmazz]

http://www.cuneiform-lang.org/

[thejmazz]

http://bionics.it/posts/the-problem-with-make-for-scientific-workflows

On pull-based versus push-based:

[thejmazz]

http://seqanswers.com/w/index.php?title=Special:Ask&offset=0&limit=10&q=%5B%5BCategory%3ABioinformatics%20application%5D%5D&p=mainlabel%3DApp.%2Fformat%3Dbroadtable&po=%3F%3DApp.%23%0A%3FNumber%20of%20citations%3DCited%0A%3FNumber%20of%20references%3DRefs.%0A%3FAltmetric%20score%3DAltmetric%0A&sort=Number_of_citations%2CNumber_of_references&order=DESC%2CDESC

[thejmazz]

https://cloud.google.com/dataflow/

[thejmazz]

About CWL (common workflow language): https://www.biostars.org/p/152226/

[thejmazz]

https://github.com/thejmazz/jmazz.me/blob/a7391bd385223dc9b9ee20f16ac0dc7122cefd65/content/post/ngs-workflow.md