workflowhub-eu / galaxy2cwl Goto Github PK

I am getting an error running the galaxy2cwl.py

  File "/usr/lib/python3.5/json/__init__.py", line 312, in loads
    s.__class__.__name__))
TypeError: the JSON object must be str, not 'bytes'

Please troubleshoot it.

Abstract CWL
Don’t have to get the types perfect, when in doubt use https://www.commonwl.org/v1.1/Workflow.html#Any
Example: https://workflowhub.eu/workflows/14/ro_crate?version=1 if you open this and look at the .cwl file, that is abstract CWL (Generated from the .ga file)
common-workflow-language/cwl-utils#27
https://github.com/PMCC-BioinformaticsCore/janis-core/blob/master/janis_core/translations/cwl.py
https://github.com/ResearchObject/ro-crate-py
CWL validation: cwltool --enable-dev --validate path/to/cwl
https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser_v1_1.py
https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/cite_extract.py
https://github.com/common-workflow-language/cwl-utils
https://gitter.im/common-workflow-language/common-workflow-language
https://workflowhub.eu/workflows/14/
Want to suggest a new Abstract CWL feature? https://github.com/common-workflow-language/common-workflow-language/issues/new
https://www.commonwl.org/user_guide/

Do we make a new release on pypi so the latest changes are included ?

do we want to keep this in the description? At this moment workflowhub will automatically parse this sentence as the description, which is not very informative.

This is a request for the API for Galaxy Community's existing workflows. As a member of the community, I am liable for including all the existing workflows into our discussion forum. If it's possible on your side, please guide me on getting the API. We can converse here, or you can mail me at [email protected]. Thanks!

(.venv) (base) beacon@2023BH01:~/workflow$ galaxy2cwl Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.ga > somatic_corkflow.cwl
Traceback (most recent call last):
File "/home/beacon/.venv/bin/galaxy2cwl", line 8, in
sys.exit(main())
File "/home/beacon/.venv/lib/python3.8/site-packages/galaxy2cwl/get_cwl_interface.py", line 287, in main
cwl_out = process_format1_json(wf_dict)
File "/home/beacon/.venv/lib/python3.8/site-packages/galaxy2cwl/get_cwl_interface.py", line 78, in process_format1_json
source_output_name = sanitize_source(input_details['output_name'])
TypeError: list indices must be integers or slices, not str

• The idea is that if i generate a cwl-abstract file now with this then, in the future, it could be updated(as in, generating a new version) when the full galaxy-cwl is working, which will produce executable cwl descriptions. So...look carefully what and how the executable cwl is being produced from galaxy in the galaxy-cwl project (see https://github.com/common-workflow-language/galaxy)

• All steps in the CWL-abstract should have the same class ? something like Galaxy_step, how does this affects the evolution of the generated cwl-abstract to the real ones in the future? what is it actually being printed as class in the cwl-galaxy project?

• The main thing that I should take into account to implement this is that all 3 ids (the one in the galaxy workflow file and the ones i set for cwl abstract in each case...from run or from static workflow), are the same in each step. -Take into account the different Galaxy workflow format versions AND the CWL versions: should I create different branches for the versions/combinations

• Datatypes: when extracting input/output datatypes from Galaxy workflow steps, can I assume these datatypes exist in CWL? otherwise is there any way to convert them to CWL types? even if its not a 1-to-1 correlation. or what is the intersection between Galaxy datatypes and CWL types?. what about Galaxy tools that define specific types?
  CWL uses ontologies to define formats. The can be from IANA (https://www.iana.org/assignments/media-types/media-types.xhtml) or EDAM (https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_1915)
  See also https://www.commonwl.org/user_guide/16-file-formats/
  For example, to indicate a bam file, it should be
  type: File
  label: Aligned sequences in BAM format
  format: edam:format_2572

• Something similar to datatypes happens with tool/job information about the operation it is performing, ideally i would like to tag that using edam, but thats only available in a handful of galaxy tools, although it should be widely available if i look in bio.tools but there is no direct link between galaxy tools and bio.tools entries