Note: This project is no longer under active development
This is a prototype conversion tool from Common Workflow Language (CWL) to Nextflow. Example workflows to demonstrate the conversion are included in the 'sample_data' folder with additional information on how to convert and run each exmaple.
- Parsing of CWL v1.0 documents.
- Basic scatter support
- Support of 'runtime' and limited supported for 'inputs' JS evaluation
- Conditional commandline inclusion.
- In CWL if an input is null it is excluded from the commandline
- Commandline parsing supports default values and prefixs
- InitialWorkDirRequirement: can handle files listed both for running locally and deployed to other compute resources.
- Parsing of CWL draft-3 or earlier specifications
- Currently each workflow step must be an individual CWL commandline tool file
- JS expressions are currently not implemented
- Record types
- outputBinding only supports 'glob'. outputEval and loadContents are unsupported.
- limited support for outputEval is now functional
- import statements do not work.
- JS expressions for File type with checksum, size, format, contents are all not supported at this time
Note: Make sure to have Java 8 installed.
Clone this repository with the following command:
git clone https://github.com/nextflow-io/cwl2nxf.git && cwl2nxf && export CWL2NXF_HOME=$PWD
Then build the project by using the following command:
Finally you can execute the
cwl2nxf application as shown below:
cd sample_data/tutorial_tar_test java -jar $CWL2NXF_HOME/build/libs/cwl2nxf-*.jar -o sample.nf wf.cwl wf.yml
sample.nf file will be created in the base folder. This file will then be runnable using Nextflow:
nextflow run sample.nf
Compile and run from sources by using the following command:
./gradlew jar ./launch.sh <wf.cwl> <wf.yml>
Debug the execution by using a remote debugger (eg. IntelliJ IDEA) as shown below:
./launch.sh -remote-debug <wf.cwl> <wf.yml>
Run the code coverage by using the command:
The generated report is available at the following path:
A comparison of native CWL graph to the Nextflow generated graph after conversion.
Nextflow graph after conversion:
The cwl2nxf is released under the Apache 2.0 License.