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4. FAQ#

4.1. How do I create non “File” types using evalFrom?#

cwlVersion: v1.0  # or v1.1
class: CommandLineTool
requirements:
  InlineJavascriptRequirement: {}

baseCommand: [ echo, "42" ]

inputs: []

stdout: my_number.txt

outputs:
  my_number:
    type: int
    outputBinding:
       glob: my_number.txt
       loadContents: True
       outputEval: $(parselnt(self[0].contents))

  my_number_as_string:
    type: string
    outputBinding:
       glob: my_number.txt
       loadContents: True
       outputEval: $(self[0].contents)

4.2. How do I rename an input file?#

This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don’t want to work with the default names that these files were given when they were created.

requirements:
  InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.src1)
        entryName: newName
      - entry: $(inputs.src2)
        entryName: $(inputs.src1.basename)_custom_extension

4.3. How do I rename an output file?#

This example demonstrates how to change the name of an output file from the default name given to it by a tool:

cwlVersion: v1.0
class: CommandLineTool
requirements:
  InlineJavascriptRequirement: {}

baseCommand: [ touch, otu_table.txt ]

inputs:
  otu_table_name: string

outputs:
 otu_table:
    type: File
    outputBinding:
      glob: otu_table.txt
      outputEval: ${self[0].basename=inputs.otu_table_name; return self;}

By modifying the basename field in the outputEval field, CWL workflow engines will rename the file using the new name for subsequent steps or as a workflow-level output.

4.4. How do I reference a local script?#

There are two ways to reference a local script:

The first method involves adding the path to a folder containing your scripts to the PATH environment variable. This allows you to execute the shell script directly (without explicitly using the sh or bash commands).

Start with adding a shebang at the top of your file:

#!/bin/bash

After that, make the script executable with the command chmod +x scriptname.sh

Finally, modify your PATH to add the directory where your script is located. (It is good practice to use $HOME/bin for storing your own scripts).

export PATH=$PATH:$HOME/bin

Now you can use baseCommand: scriptname.sh to run the script directly.

#!/bin/bash
cwlVersion: v1.0
class: CommandLineTool
baseCommand: scriptname.sh

When you wish to share your work later, you can place your script in a software container in the Docker format.

The second method involves including an input of type: File in the script itself:

class: CommandLineTool

inputs:
  my_script:
     type: File
     inputBinding:
        position: 0


  # other inputs go here

baseCommand: sh

outputs: []

4.5. How can I set self-based input bindings for optional inputs?#

Currently, cwltool can’t cope with missing optional inputs if their input binding makes use of self. Below is an example workaround for this, pending a more sophisticated fix.

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

requirements: { InlineJavascriptRequirement: {} }

inputs:
  cfg:
    type: File?
    inputBinding:
      prefix: -cfg
      valueFrom: |
        ${ if(self === null) { return null;} else { return self.basename; } }

baseCommand: echo

outputs: []

4.6. How can I model a “one-or-the-other” parameter?#

Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter.

cwlVersion: v1.0
class: CommandLineTool
requirements:
  InlineJavascriptRequirement: {}
inputs:
  fancy_bool:
     type: boolean
     default: false  # or true
     inputBinding:
        valueFrom: ${if (self) { return "foo";} else { return "bar";}}

baseCommand: echo

outputs: []

4.7. How do I connect a solo value to an input that expects an array of that type?#

Add a MultipleInputFeatureRequirement along with linkMerge: merge_nested:

merge_nested

The input must be an array consisting of exactly one entry for each input link. If “merge_nested” is specified with a single link, the value from the link must be wrapped in a single-item list.

Which means “create a list with exactly these sources as elements”.

Or in other words: if the destination is of type File[] (an array of Files) and the source is a single File then add MultipleInputFeatureRequirement to the Workflow level requirements and add linkMerge: merge_nested under the appropriate in entry of the destination step.

cwlVersion: v1.0
class: Workflow

requirements:
  MultipleInputFeatureRequirement: {}

inputs:
  readme: File

steps:
  first:
    run: tests/checker_wf/cat.cwl
    in:
     cat_in:  # type is File[]
       source: [ readme ]  # but the source is of type File
       linkMerge: merge_nested
    out: [txt]

outputs:
  result:
    type: File
    outputSource: first/txt

4.8. How do make an input optional? 💯#

To make an input parameter optional, add a question mark to the type declaration.

inputs:
  InputRead1:
    type: File
    inputBinding:
      position: 100

  #Optional Inputs
  isCasava:
    type: boolean?
    inputBinding:
      position: 1
      prefix: "--casava"

4.9. How do I specify an input that must come from a list of predefined values (i.e. How do I use enum inputs) ?#

For command line flags that require a specific input as the argument an enum type can be declared in CWL. Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.

Format:
  type:
    - "null"
    - type: enum
      symbols:
        - bam
        - sam
        - bam_mapped
        - sam_mapped
        - fastq
  inputBinding:
    position: 2
    prefix: "--format"

4.10. How do I describe dependent or exclusive input parameters(e.g. How do I use record inputs)?#

For commandline flags that are either mutually exclusive or dependent a special record type can be defined. You can also specify null here to create optional inputs.

#Using record inputs to create mutually exclusive inputs

  Strand:
    type:
      - "null"
      - type: record
        name: forward
        fields:
          forward:
              type: boolean
              inputBinding:
                prefix: "--fr-stranded"

      - type: record
        name: reverse
        fields:
          reverse:
            type: boolean
            inputBinding:
              prefix: "--rf-stranded"

  PseudoBam:
    type: boolean?
    inputBinding:
      prefix: "--pseudobam"

#Using record inputs to create dependent inputs

  GenomeBam:
    type:
      - "null"
      - type: record
        name: genome_bam
        fields:
          genomebam:
            type: boolean
            inputBinding:
              prefix: "--genomebam"

          gtf:
            type: File
            inputBinding:
              prefix: "--gtf"

          chromosomes:
            type: File
            inputBinding:
              prefix: "--chromosomes"

4.11. How do I set mutually exclusive parameters?#

To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value.

steps:

  build_hisat2_index:
    run: ../Tools/Hisat2-Index.cwl
    in:
      InputFiles:
        source: FastaFiles
        valueFrom : |
          ${return {"fasta": self};}

      IndexName: IndexName

    out: [indexes]

4.12. How can I set Booleans?#

These can be set by using the default field

input:
  default: true

4.13. What should I do when concatenating strings in inputs?#

The valueFrom field must be used instead of default.

input:
  valueFrom: |
     My String: $(input.stringvalue)

4.14. I get cwltool errors due to filenames with space characters inside. What should I do?#

cwltool does not allow some characters in filenames by default.

For example, the filename a space is here.txt includes 3 space characters.

ERROR Workflow error, try again with --debug for more information:

Invalid filename: 'a space is here.txt' contains illegal characters

If you can not avoid these dangerous characters, then pass --relax-path-checks to cwltool.

4.15. What should I do when I get CWL Parameter Reference error due to hyphen in an input identifier?#

If cwltool --validate returns valid

$ cwltool --validate cwl/qiime.cwl
INFO /usr/local/bin/cwltool 1.0.20190831161204
INFO Resolved 'cwl/qiime.cwl' to 'file:///workspace/cwl/qiime.cwl'
cwl/qiime.cwl is valid CWL.

But executing it causes an error like:

$ cwltool cwl/qiime.cwl --sample-input metadata.tsv
INFO /usr/local/bin/cwltool 1.0.20190831161204
INFO Resolved 'cwl/qiime.cwl' to 'file:///workspace/cwl/qiime.cwl'
ERROR Workflow error, try again with --debug for more information:
cwl/qiime.cwl:14:5: Expression evaluation error:
                    Syntax error in parameter reference '(inputs.sample-input)'. This could be due
                    to using Javascript code without specifying InlineJavascriptRequirement.

The file is here

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [qiime, metadata, tabulate]
arguments:
  - prefix: --m-input-file
    valueFrom: $(inputs.sample-input)
inputs:
  sample-input: File
outputs: []

Problem caused by - (hyphen character).

valueFrom: $(inputs.sample-input)
                        # ^ this is problem
...

inputs:
  sample-input: File
      # ^ this is problem

To fix this error, change - (hyphen) to _ (underscore):

valueFrom: $(inputs.sample_input)
                        # ^ changed here

...

inputs:
  sample_input: File
      # ^ changed here

If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:

valueFrom: $(inputs["sample-input"])

4.16. How do I use CWL and cwltool with Singularity?#

The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards.

4.17. How do I debug the JavaScript in my CWL tool?#

You can use the –js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8

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