positional arguments:¶

workflow job_order

optional arguments:¶

-h, --help

show this help message and exit

--basedir BASEDIR

--outdir OUTDIR

Output directory, default current directory

--no-container

Do not execute jobs in a Docker container, even when specified by the CommandLineTool

--preserve-environment ENVVAR

Preserve specific environment variable when running CommandLineTools. May be provided multiple times.

--preserve-entire-environment

Preserve entire parent environment when running CommandLineTools.

--rm-container

Delete Docker container used by jobs after they exit (default)

--leave-container

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

--cachedir CACHEDIR

Directory to cache intermediate workflow outputs to avoid recomputing steps.

--rm-tmpdir

Delete intermediate temporary directories (default)

--leave-tmpdir

Do not delete intermediate temporary directories

--move-outputs

Move output files to the workflow output directory and delete intermediate output directories (default).

--leave-outputs

Leave output files in intermediate output directories.

--copy-outputs

Copy output files to the workflow output directory, don't delete intermediate output directories.

--enable-pull

Try to pull Docker images

--disable-pull

Do not try to pull Docker images

--rdf-serializer RDF_SERIALIZER

Output RDF serialization format used by --print-rdf (one of turtle (default), n3, nt, xml)

--eval-timeout EVAL_TIMEOUT

Time to wait for a Javascript expression to evaluate before giving an error, default 20s.

--print-rdf

Print corresponding RDF graph for workflow and exit

--print-dot

Print workflow visualization in graphviz format and exit

--print-pre

Print CWL document after preprocessing.

--print-deps

Print CWL document dependencies.

--print-input-deps

Print input object document dependencies.

--pack

Combine components into single document and print.

--version

Print version and exit

--validate

Validate CWL document only.

--strict

Strict validation (unrecognized or out of place fields are error)

--non-strict

Lenient validation (ignore unrecognized fields)

--verbose

Default logging

--quiet

Only print warnings and errors.

--debug

Print even more logging

--tool-help

Print command line help for tool

--relative-deps {primary,cwd}

When using --print-deps, print paths relative to primary file or current working directory.

--enable-dev

Allow loading and running development versions of CWL spec.

--default-container DEFAULT_CONTAINER

Specify a default docker container that will be used if the workflow fails to specify one.

--no-match-user

Disable passing the current uid to 'docker run --user`

--disable-net

Use docker's default networking for containers; the default is to enable networking.

--custom-net CUSTOM_NET

Will be passed to `docker run` as the '--net' parameter. Implies '--enable-net'.

--on-error {stop,continue}

Desired workflow behavior when a step fails. One of 'stop' or 'continue'. Default is 'stop'.

--compute-checksum

Compute checksum of contents while collecting outputs

--no-compute-checksum

Do not compute checksum of contents while collecting outputs

--relax-path-checks

Relax requirements on path names. Currently allows spaces.