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README.md

Makeflow Examples Repository

This is an repository of sample workflows for use with the Makeflow workflow system. You can use as examples of how to use Makeflow, or to benchmark the performance of your system. If you have an interesting workflow, we would be happy to add it here; please make a pull request.

We recommend the following citation for this data:

Nick Hazekamp and Douglas Thain, Makeflow Examples Repository, http://github.com/cooperative-computing-lab/makeflow-examples, 2017.

Some of these examples are more complete than others, as described in the README.md files in each directory:

  • BLAST, SSAHA, BWA, HECIL, BWA-GATK, SHRIMP, and Shakespeare contain complete instructions for downloading software, generating sample data, and creating and running complete workflows from scratch. Each workflow is demonstrated in two ways: once using the classic make language (.mf file) and again using the JX language (.jx file).

  • LIFEMAPPER and SNPEXP are static snapshots of just the workflow structure, but do not contain the applications and data necessary to execute them. You may find them instructive as further examples of how to write workflows.

  • It should be noted that the sample data that is generated in these is complelely random and has no value other than for showing workflow performance. Some analysis programs may emit errors indicating low quality data.

BLAST workflow adapted from the Biocompute web portal. (Shown at a scale of 10 splits.)
SSAHA genomics analysis workflow, courtesy of Scott Emrich and Notre Dame Bioinformatics Laboratory. (Shown at scale of 25 splits.)
BWA genomics analysis workflow, courtesy of Scott Emrich and Notre Dame Bioinformatics Laboratory. (Shown at scale of 20 splits.)
SHRIMP genomics analysis workflow adapted from the Biocompute web portal. (Shown at a scale of 100 splits.)
HECIL genomics analysis workflow, courtesy of Olivia Choudhury and Connor Howington.
Lifemapper Species Distribution Modeling (SDM) workflow, courtesy of C.J. Grady. (Shown at scale of 10 species and 5 random trials.)
SNPEXP Genomics analysis workflow courtesy of Scott Emrich and Notre Dame Bioinformatics Laboratory.
BWA-GATK genomics workflow by Nick Hazekamp and Olivia Choudhury.
Example text analysis workflow by Nate Kremer-Herman.

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Example workflows for the Makeflow workflow system.

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