prasunanand/CWL-workflows

Workflows written in common workflow language (CWL)

CWL-workflows

Workflows written in common workflow language (CWL)

Run a workflow

(Plesae see how to install cwltool: https://github.com/common-workflow-language/cwltool)

To run a workflow named test-workflow.cwl, type as follows:

cwltool Workflows/test-workflow.cwl Jobs/small.ERR034597.test-workflow.yml

When you use toil

virtualenv -p python2 env2
. env2/bin/activate
pip install toil[cwl]
toil-cwl-runner Workflows/test-workflow.cwl Jobs/small.ERR034597.test-workflow.yml

Functional equivalence (FE) of genome sequencing analysis pipelines

I will write CWL workflows that are consistent with the FE standard described in PMID: 30279509

For example, I use bwa-mem (v0.7.15-r1140) with the parameters “-K 100000000 -p -Y”.

Visualize test-workflow.cwl

(Visualize at 2018-12-12 using CWL Viewer https://view.commonwl.org)