CWL in Toil

The Common Workflow Language (CWL) is an emerging standard for writing workflows that are portable across multiple workflow engines and platforms. Toil has full support for the CWL v1.0.1 specification.

Running CWL Locally

To run in local batch mode, provide the CWL file and the input object file:

$ toil-cwl-runner example.cwl example-job.yml

For a simple example of CWL with Toil see Running a basic CWL workflow.

Running CWL in the Cloud

To run in cloud and HPC configurations, you may need to provide additional command line parameters to select and configure the batch system to use.

To run a CWL workflow in AWS with toil see Running a CWL Workflow on AWS.

Running CWL within Toil Scripts

A CWL workflow can be run indirectly in a native Toil script. However, this is not the standard way to run CWL workflows with Toil and doing so comes at the cost of job efficency. For some use cases, such as running one process on multiple files, it may be useful. For example, if you want to run a CWL workflow with 3 YML files specifying different samples inputs, it could look something like:

from toil.job import Job
from toil.common import Toil
import subprocess
import os

def initialize_jobs(job):

def runQC(job, cwl_file, cwl_filename, yml_file, yml_filename, outputs_dir, output_num):
    tempDir = job.fileStore.getLocalTempDir()

    cwl = job.fileStore.readGlobalFile(cwl_file, userPath=os.path.join(tempDir, cwl_filename))
    yml = job.fileStore.readGlobalFile(yml_file, userPath=os.path.join(tempDir, yml_filename))

    subprocess.check_call(["cwltoil", cwl, yml])

    output_filename = "output.txt"
    output_file = job.fileStore.writeGlobalFile(output_filename)
    job.fileStore.readGlobalFile(output_file, userPath=os.path.join(outputs_dir, "sample_" + output_num + "_" + output_filename))
    return output_file

if __name__ == "__main__":
    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")
    options.logLevel = "INFO"
    options.clean = "always"
    with Toil(options) as toil:

        # specify the folder where the cwl and yml files live
        inputs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "cwlExampleFiles")
        # specify where you wish the outputs to be written
        outputs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "cwlExampleFiles")

        job0 = Job.wrapJobFn(initialize_jobs)

        cwl_filename = "hello.cwl"
        cwl_file = toil.importFile("file://" + os.path.abspath(os.path.join(inputs_dir, cwl_filename)))

        # add list of yml config inputs here or import and construct from file
        yml_files = ["hello1.yml", "hello2.yml", "hello3.yml"]
        i = 0
        for yml in yml_files:
            i = i + 1
            yml_file = toil.importFile("file://" + os.path.abspath(os.path.join(inputs_dir, yml)))
            yml_filename = yml
            job = Job.wrapJobFn(runQC, cwl_file, cwl_filename, yml_file, yml_filename, outputs_dir, output_num=str(i))