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)