How do I pass literals in CWL workflows?

Question

[thomas.e]

I want to pass a literal to a tool, for example, the number of threads, in a workflow step.

The parameter is defined as an optional int in the tool itself:

  threads:
    type: int?
    inputBinding:
      prefix: --threads

If I do this in the workflow:

      threads:
        valueFrom: 4

cwltool complains that the value is an int and should be a string.

(p) [thomas.e@vc7hpc-040 test]$ cwltool --debug ../src/pdx-pl.cwl --read1 ../data/S1_R1.fastq.gz --read2 ../data/S1_R2.fastq.gz 
/stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/p/bin/cwltool 1.0.20170721221557
Resolved '../src/pdx-pl.cwl' to 'file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl'
Tool definition failed validation:
../src/pdx-pl.cwl:3:1: Object ../src/pdx-pl.cwl is not valid because
                         tried Workflow but
../src/pdx-pl.cwl:102:1:     the steps field is not valid because
                               tried array of <workflowstep> but
../src/pdx-pl.cwl:503:3:         item is invalid because
../src/pdx-pl.cwl:506:5:           the in field is not valid because
../src/pdx-pl.cwl:525:7:             item is invalid because
../src/pdx-pl.cwl:526:9:               the valueFrom field is not valid because
                                         - tried string but
                                             the value is not string
                                         - tried Expression but
                                             value is a int but expected a string

If I pass a string it complains that it is not an int

[step trim] start
Exception on step 'trim'
[step trim] Cannot make job: Invalid job input record:
the nthreads field is not valid because
  tried int but
    '4' is not int

Currently, I using JS but it seems it should be easier:

      threads:
        valueFrom: ${ return 27; }

[wolfganggerlach1981]

how about

valueFrom: $( 27 )

that is a bit easier :-)

To me this looks like a bug in the CWL implementation as your 4 should be interpreted as an int 4. But I did not test it myself so I can't tell for sure.

[wolfganggerlach1981]

ah, valueFrom can only be a string or an expressson, according to the docs. That is your problem.

[thomas.e]

So a case of "broken as designed". Seems to me other literals should be allowed.

Answer 1

[awilke1972]

an other option is adding a default:

threads: type: int? default: 4 inputBinding: prefix: --threads

[thomas.e]

I think this is only for the CommandLineTool where it is not appropriate to set a default.

[Michael R. Crusoe]

This is how I pass literals in Workflows, see https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/master/workflows/emg-pipeline-v3.cwl#L194