Tests to figure out how to use CWL in a complex directory structure

Wait until CWLTool gets fixed

document what --basedir does #278 (open since 2017) "--basedir" option is not working #668 (open since 2018)

Symlink config files

Place the input file where the relative paths make sense. e.g.:

cd study
ln -sr code/dummy.yml rawdata/sub-01/ses-01/
cwltool --outdir derivatives/sub-01/dummy code/dummy.cwl rawdata/sub-01/ses-01/dummy.yml

PROS: simple, developer-friendly CONS: file copies everywhere, one config per session, input file is not configurable

TODO: Config file templates

Copy Jinja-parsed instances of the input file to the working directory.

PROS: provenance record CONS: file copies everywhere, one config per session, requires external templating engine

Flatten Inputs

Use relpaths2files.cwl to stage files in a complex tree to working directory.

cwltool --outdir derivatives/sub-02/dummy code/wrapped_dummy.cwl code/wrapped_dummy.yml

PROS: potential for workflow config (scatter over Directories?), might need to be modified to use name globbing CONS: clunky, hacky

TODO: Snakemake workflow for CWL tools?