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Patterns commonly encountered when writing CWL workflows

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CWL patterns
------------

_Some patterns commonly encountered when writing CWL workflows_

- [Manifest file via Javascript](#manifest-file-via-javascript)
- [Embedding scripts](#embedding-scripts)
    - [I have my script in a separate file](#i-have-my-script-in-a-separate-file)
    - [I have `$` signs in my script :(](#i-have--signs-in-my-script-)
    - [I don't want to escape the `$`](#i-dont-want-to-escape-the-)
- [Embedding a bash script (style 2)](#embedding-a-bash-script-style-2)
- [Manipulating a list of files using expressions](#manipulating-a-list-of-files-using-expressions)
- [Link input files to working directory](#link-input-files-to-working-directory)
- [How to handle port type mismatches](#how-to-handle-port-type-mismatches)

[Which of the Workflow Patterns Initiative patterns does CWL support?](workflow_patterns_initiative/README.md)

## Manifest file via Javascript
> My tool takes in a list of filenames as input. I used to pass each file name
> on the command line, but when I scale up I run into unix  "Argument list too
> long"  errors. What can I do?

If the program accepts, or can be altered to accept, a manifest file containing
a list of input file paths, the CWL can be written to generate this manifest
file on the fly before invoking the tool ([example](manifest.cwl)).

## Embedding scripts
> I have a Python script that I want to embed in my tool wrapper (not make part
> of the docker image). How would I do this?

You can embed the script as an `InitialWorkDirRequirement`
([example](embed.cwl)).

### I have my script in a separate file
> I use good software practices. My Python/Ruby/Haskell/... script is in a
> separate file from my CWL wrapper.

You can use the `$include` directive to pull in the file into your CWL.
You can use it in `InitialWorkDirRequirement`
([example](include-file/external-python.cwl)) or in File Contents ([example](include-file/external-python-no-expansion.cwl))

### I have `$` signs in my script :(
> My embedded (Bash/Python/R) script has "$" signs in it and this is conflicting
> with CWL parameter references. How do get them to play nicely together?

You can escape the `$` in your script with `\$`

### I don't want to escape the `$`
> I'd rather just paste the script into the CWL and not have to go through it, 
> escaping the "$" signs. Do I have another option?

You could embed your script in the "contents" field of the default value of a
file. To note in this solution is that a user can supply a different file to the
script input and override the default script. This can be considered a bug or a
feature, depending on your use case ([example](embed2.cwl)).

## Embedding a bash script (style 2)

A bash script can be passed as a string via the command line and invoked from
the command line.  ([example](list-of-files-bash.cwl)).

## Manipulating a list of files using expressions
> I have an input that is a list of files. I wish to do processing based on the
> file paths.

This depends a bit on what the expression is intended to do. The easiest is if
the whole processing can be done in javascript. In this case the pattern looks
like

```
${
  var cmd = "";
  for( var i = 0; i < inputs.files.length; i++) {
     cmd += "\n echo " + inputs.files[i].path;
  }
  return cmd;  
}
```
([example](list-of-files-1.cwl))

This works well for when we can do with a JSON or simple string return value
from the JS code. If what we really want is an embedded script (say a bash or
Python script) to be generated, say via the `InitialWorkDirRequirement` it
becomes cumbersome to write in this fashion. One way of doing this is to write a
succinct JS expression that converts the passed JSON object into a list of paths
in the syntax accepted by the script.

Here is an example for [Python](list-of-files-python.cwl) and for
[bash](list-of-files-bash.cwl)

## Link input files to working directory
> I have a tool that does not do well with arbitrary file paths. I'd like to
> link the files into the working directory so I don't have to deal with
> arbitrary mount paths and so on.

You can use `InitialWorkDirRequirement` to link the files
([example](stage-files.cwl)).

You can mix this with embedding scripts
([example](embed-script-and-stage-files.cwl)).

## How to handle port type mismatches

- Tool A produces a list of Files (or strings, ints ...) 
- Tool B accepts only a single File (or string, int ...)
- How do I connect A to B?

If you are _sure_ this is not going to be a problem, e.g. in this context A will
only ever produce one file, or you are only interested in one file, you can use
a step `valueFrom` expression to convert the types.

[Here](port-matching/workflow.cwl) is a workflow that will raise validation
warnings and will fail on execution because of port type mismatches.

[Here](port-matching/workflow-value-from.cwl) is the same workflow with
`valueFrom` added to make the port types match.

## Some commonly used Javascript expression tools
You can tailor the input/output types to your situation.

### Flatten a nested array into an array
[flatten-nestedarray.cwl](javascript_snippets/flatten-nestedarray.cwl) shows how to flatten an
array such as \[\["a0", "a1"\], \["b0", "b1"\]\] into \["a0", "a1", "b0", "b1"\].

### Divide an array into batches with a given batch size
[batch-array.cwl](javascript_snippets/batch-array.cwl) shows how to divide an array such as
\["a0", "a1", "a2", "a3", "a4"\] into a nested array
\[\["a0", "a1"\], \["a2", "a3"\], \["a4"\]\] with batch size 2. With batch size
3, the batched nested array would be [\["a0", "a1", "a2"\], \["a3", "a4"\]\].

### Stage an array of 'File' and 'Directory' type in a 'Directory'
[array-to-dir.cwl](javascript_snippets/array-to-dir.cwl) shows how to stage an array such as
\[file0, dir0, file1, dir1\] in a new directory, with file0, dir0, file1, dir1
as its content.

### Stage a nested array of 'File' and 'Directory' type in a 'Directory'
[nestedarray-to-dir.cwl](javascript_snippets/nestedarray-to-dir.cwl) shows how to stage a nested array
such as \[\[file0, dir0\], \[file1, dir1\]\] in a new directory, with
file0, dir0, file1, dir1 as its content.

### Process a directory of bgzipped and indexed vcf files into an array
[get-vcfs.cwl](javascript_snippets/get-vcfs.cwl) is a bioinformatics specific tool that
processes a 'Directory' with files such as a.vcf.gz, a.vcf.gz.tbi, b.vcf.gz,
b.vcf.gz.tbi into an array \[a.vcf.gz, b.vcf.gz\], where a.vcf.gz.tbi is
the secondary file of a.vcf.gz, and b.vcf.gz.tbi is the secondary file of
b.vcf.gz, respectively.

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