Converter from the Broad Institute's Workflow Definition Language (WDL) to the Common Workflow Language. References: CWL spec https://github.com/common-workflow-language/common-workflow-language WDL spec https://github.com/broadinstitute/wdl Python WDL parser https://github.com/broadinstitute/pywdl cwl2wdl (convert the other way) https://github.com/adamstruck/cwl2wdl wdl2cwl is being actively developed! Please report bugs ============================== NOTES ON AUTOCONVERTING Runtime (WDL) docker [] -> DockerRequirement, only one image resources -> ResourceRequirement, megabytes -> mebibytes string If the output {...} section is omitted, then the workflow includes all outputs from all calls in its final output. secondaryFiles - .fai - ^.dict resource and docker requirements: megabytes vs mebibytes read_X() functions: if an input parameter is read from a file by a function like read_tsv or read_csv, it must start with a backslash. wdl2cwl has to transform file inputs in plain strings to a CWL File object. wdl2cwl only recognizes a filepath in a .txt file if it starts with a backslash. Moreover, all strings starting with '/' will be treated as filepathes.