Starting CWL with `Zatsu` method!

What is Zatsu method?

Zatsu (雑 in Japanese) is translated into the following English words:

• rough
• crude
• sloppy
• messy

Zatsu method is a way to achieve the objective (writing a CWL, in this article) without knowing the details and without considering the details as much as possible.

What is this article?

If you are a serious person, this article is not for you. You should go to the User Guide and the specifications which will help you to write a graceful CWL.

This article is for the people who complain: I do not want to care about the details of the CWL syntax! I just want to put my tool into CWL workflows!.
This article describes how to write a tool definition in Common Workflow Language (CWL) without knowing details of the specifications.

This is an English version of 雑に始める CWL！ that is written in Japanese.

Notice

This article does not describe the way to handle tool options gracefully. Go to the User Guide.

A tool to be CWLized in this article

The following command print the first n lines to the standard output.
n is specified with -n option.

$ head -n5 foobar.txt

• I want to give 5 in -n5 and foobar.txt as input parameters of CWL definition.
• I want to capture the standard output of head command as an output object.
• I do not care about other options!

Running example of head command (without CWL)

$ man head > manhead.txt
$ head -n5 manhead.txt

HEAD(1)                   BSD General Commands Manual                  HEAD(1)

NAME
     head -- display first lines of a file

Let's cooking!

• First, copy the following as head.cwl.

head.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: []
arguments: []
inputs: []
outputs: []

• Add the first part of the command to baseCommand and the rest to arguments (comma separated).

head.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [head]
arguments: [-n5, foobar.txt]
inputs: []
outputs: []

• Add input parameters to inputs field. In this case, you introduce source for the input file and nlines to specify the first n lines.

head.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [head]
arguments: [-n5, foobar.txt]
inputs:
  - id: source
  - id: nlines
outputs: []

• Add a type for each input parameter. Specify File type for source because it takes a file and specify int for nlines because it takes an integer.

head.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [head]
arguments: [-n5, foobar.txt]
inputs:
  - id: source
    type: File
  - id: nlines
    type: int
outputs: []

• Replacing 5 and foobar.txt with the values of nlines and source. It can be done by using the following notation: $(inputs."id field name").

head.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [head]
arguments: [-n$(inputs.nlines), $(inputs.source)]
inputs:
  - id: source
    type: File
  - id: nlines
    type: int
outputs: []

• Add an output parameter. In this case I call it out.

head.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [head]
arguments: [-n$(inputs.nlines), $(inputs.source)]
inputs:
  - id: source
    type: File
  - id: nlines
    type: int
outputs:
  - id: out

• As same as the case of input parameters, add a type for each output parameter. You can use stdout type to capture the standard output.

head.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [head]
arguments: [-n$(inputs.nlines), $(inputs.source)]
inputs:
  - id: source
    type: File
  - id: nlines
    type: int
outputs:
  - id: out
    type: stdout

• Well done!

Does it work?

Let's run it with source=manhead.txt and nlines=5 as input parameters.

$ man head > manhead.txt
$ cwltool head.cwl --source manhead.txt --nlines 5
...
[job head.cwl] completed success
{
    "out": {
        "location": "file:///Users/tom-tan/147d6ad946430f35c2aafbff6c5604d43b30aa14",
        "basename": "147d6ad946430f35c2aafbff6c5604d43b30aa14",
        "class": "File",
        "checksum": "sha1$30c2a20de147871db76e237705ac274277504428",
        "size": 145,
        "path": "/Users/tom-tan/147d6ad946430f35c2aafbff6c5604d43b30aa14"
    }
}
Final process status is success
$ cat 147d6ad946430f35c2aafbff6c5604d43b30aa14

HEAD(1)                   BSD General Commands Manual                  HEAD(1)

NAME
     head -- display first lines of a file

• You can see the output object after [job head.cwl] completed success.
  • You can see the file object named 147d6ad9464... for out parameter.
• You can verify it is the same output of [Running example of head command (without CWL)](#Running example of head command (without CWL)) by using cat command.

Next steps!

How terrible the output file name is...

You can specify the file name by using stdout field.

head.cwl

...
outputs:
  - id: out
    type: stdout
stdout: output.txt # Add this line

I want to specify the output file name to manhead-head.txt when the source file name is manhead.txt.

Use $() notation. You can get manhead from manhead.txt by using nameroot field in File object.

head.cwl

...
outputs:
  - id: out
    type: stdout
stdout: $(inputs.source.nameroot)-head.txt # Add this line

Can I use Docker?

Yes, use DockerRequirement. You can specify the docker image by using dockerPull field.

head.cwl

...
outputs:
  - id: out
    type: stdout
stdout: $(inputs.source.nameroot)-head.txt
# Add the following
requirements:
  - class: DockerRequirement
    dockerPull: debian:latest

You do not have to specify the details of containers such as volume mount.
They can be handled by CWL workflow engines.

Conclusion

Now you can write tool definitions in CWL!
Do it!