[wip] simple input object generation

[mr-c]

Inspired by Dockstore's equivalent feature

Will close #384

[ctb]

Note that

cwltool --make-template https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/Dockstore.cwl > params.yaml

succeeds but shows the following error message that made me think it did not succeed:

/home/tx160085/env/bin/cwltool 1.0
https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/Dockstore.cwl:3:1: unrecognized extension field `http://purl.org/dc/terms/creator`.  Did you include a $schemas section?

Any way to change this to a warning, or be more verbose about the fact that params.yml is legit?

[ctb]

Also - the dockstore output includes a section for the output file, e.g. bamstats_report in the example that ngs-docs/2017-cloud-workflows-misc#1 is modifying. This doesn't seem to be the case with the --make-template command. Is that what you mean in this comment by uses the standardized --outdir option? thx!

[mr-c]

@ctb thank you for the verification. This is incomplete but I'll release it for later improvement :-)

Re: output file name in the input object -- yes, that is a dockstore specific extension (and one that I never personally understood). Use the standardized --outdir if you'd like to put your outputs anywhere besides the current working directory. If you'd like to discover the filename of a particular output you can parse the output JSON to find out (some workflows the file names vary).

[mr-c]

re: the warning, this is a known regression #455

[denis-yuen]

@ctb @mr-c FYI, the output file name is for specifying an output location https://dockstore.org/docs/advanced-features#file-provisioning

Note that putting it in /tmp works but is probably a less interesting example than putting the output into S3, Synapse, etc. (if you have the plugins installed)

[mr-c]

@denis-yuen Ah, that makes more sense. It would be more portable if you added these as a dockstore specific directives, otherwise it looks like another input which is confusing to CWL runners and humans alike:

Example:

bam_input:
    class: File
    path: /tmp/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
dockstore:outputs:
    bamstats_report:
        class: File
        path: /tmp/bamstats_report.zip

This should be proposed as a standardized optional feature, then dockstore:outputs could become cwl:outputs

[denis-yuen]

@mr-c I think that would be a reasonable improvement. It would simplify our code too.