Add workflow file to crate.
Correct path to output files in metadata file.
Add CreateActions for tool executions.
Add ControlActions.
Add SoftwareApplications for processes.
Add HowToSteps.
Add agent information (orcid, name) to nextflow.config that is incorporated into metadata file.

Use outdir from config as publishDir
Remove nested list for createAction results
Correct controlAction id

Add license information according to Workflow RO-Crate
Handle parameters set in workflow
Add PropertyValue for FormalParameters
Add PropertyValue to object field for CreateAction of workflow
Add nextflow_schema.json to outdir if present

* Add objects to CreateActions
* Add license entity if license information in nextflow.config is a valid URL
* Fix bug: Don't add unpublished files to CreateAction results. Causes NullPointerException, as they aren't contained in workflowOutputs map

* (Hopefully) all input/output files are now copied into the crate
* Add Intermediate results ro-crate-metadata.json
* Add nextflow.config to ro-crate-metadata.json
* Add datePublished to Dataset
* valid RO-Crate according to rocrate-validator

Signed-off-by: fbartusch <[email protected]>

* Change HowToStep position to string
* Remove nextflow.config object from OrganizeAction
* add author to root data entity
* passes roc-validator with severity REQUIRED

Signed-off-by: fbartusch <[email protected]>