DESCRIPTION

usage: main.py [-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

--conformance-test

--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 VAR1 [VAR2 ...]

Preserve specified environment variables 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

--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.

--enable-pull

Try to pull Docker images

--disable-pull

Do not try to pull Docker images

--dry-run

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-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 from $import, $include, $schemas

--version

Print version and exit

--update

Update to latest CWL version, print and exit

--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