cwltool(1) Refefence executor for Common Workflow Language


usage: [-h] [--conformance-test] [--basedir BASEDIR] [--outdir OUTDIR]
[--no-container] [--preserve-environment VAR1 [VAR2 ...]] [--rm-container | --leave-container] [--tmpdir-prefix TMPDIR_PREFIX] [--tmp-outdir-prefix TMP_OUTDIR_PREFIX] [--rm-tmpdir | --leave-tmpdir] [--move-outputs | --leave-outputs] [--enable-pull | --disable-pull] [--dry-run] [--rdf-serializer RDF_SERIALIZER] [--print-rdf | --print-dot | --print-pre | --print-deps | --version | --update] [--strict | --non-strict] [--verbose | --quiet | --debug] [--tool-help] [workflow] ...

positional arguments:

workflow job_order

optional arguments:

-h, --help
show this help message and exit
--basedir BASEDIR
--outdir OUTDIR
Output directory, default current directory
Do not execute jobs in a Docker container, even when specified by the CommandLineTool
--preserve-environment VAR1 [VAR2 ...]
Preserve specified environment variables when running CommandLineTools
Delete Docker container used by jobs after they exit (default)
Do not delete Docker container used by jobs after they exit
--tmpdir-prefix TMPDIR_PREFIX
Path prefix for temporary directories
--tmp-outdir-prefix TMP_OUTDIR_PREFIX
Path prefix for intermediate output directories
Delete intermediate temporary directories (default)
Do not delete intermediate temporary directories
Move output files to the workflow output directory and delete intermediate output directories (default).
Leave output files in intermediate output directories.
Try to pull Docker images
Do not try to pull Docker images
Load and validate but do not execute
--rdf-serializer RDF_SERIALIZER
Output RDF serialization format used by --print-rdf (one of turtle (default), n3, nt, xml)
Print corresponding RDF graph for workflow and exit
Print workflow visualization in graphviz format and exit
Print CWL document after preprocessing.
Print CWL document dependencies from $import, $include, $schemas
Print version and exit
Update to latest CWL version, print and exit
Strict validation (unrecognized or out of place fields are error)
Lenient validation (ignore unrecognized fields)
Default logging
Only print warnings and errors.
Print even more logging
Print command line help for tool