Workflows written in common workflow language (CWL)
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
DATA
Jobs
Tools
Workflows
LICENSE
README.md

README.md

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)

test-workflow.cwl