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Convert faq headings to questions (#358)
* change FAQ heading 3 to question * change FAQ heading 4 to question * change FAQ heading 5 to question * change faq 6 to heading * change faq 7 to heading * change faq 8 to heading * change faq 9 to heading * change faq 10 to heading * modify faq 9 * change faq 11 heading to question * change faq 12 heading to question * change faq 13 heading to question * change faq 14 & 15 headings to questions * change faq 16 heading to question * change faq 1 heading to question * adust punctuation and capitalisation * updates from review --------- Co-authored-by: Peter Amstutz <[email protected]>
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src/faq.md

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:backlinks: "top"
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```
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## Non "`File`" Types Using `evalFrom`
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## How do I create non "`File`" types using `evalFrom`?
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```yaml
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cwlVersion: v1.0 # or v1.1
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outputEval: $(self[0].contents)
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```
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## Rename an Input File
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## How do I rename an input file?
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This example demonstrates how to change the name of an input file
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as part of a tool description.
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entryName: $(inputs.src1.basename)_custom_extension
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```
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## Rename an Output File
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## How do I rename an output file?
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This example demonstrates how to change the name of an output file
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from the default name given to it by a tool:
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outputEval: ${self[0].basename=inputs.otu_table_name; return self;}
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```
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## Referencing a Local Script
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## How do I reference a local script?
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There are two ways to reference a local script:
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In CWL, everything must be directly stated.
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```
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## Setting `self`-based Input Bindings for Optional Inputs
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## How can I set `self`-based input bindings for optional inputs?
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Currently, `cwltool` can't cope with missing optional inputs if their
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input binding makes use of `self`.
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outputs: []
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```
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## Model a "one-or-the-other" Parameter
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## How can I model a "one-or-the-other" parameter?
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Below is an example showing how
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to specify different strings to be added to a command line,
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outputs: []
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```
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## Connect a Solo Value to an Input that Expects an Array of that Type
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## How do I connect a solo value to an input that expects an array of that type?
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Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)
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along with
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type: File
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outputSource: first/txt
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```
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## Optional Inputs 💯
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## How do make an input optional? 💯
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To make an input parameter optional, add a question mark to the type declaration.
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prefix: "--casava"
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```
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<a name="enuminputs"></a>
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## Enum Inputs ⚜️
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## How do I specify an input that must come from a list of predefined values (i.e. How do I use enum inputs) ?
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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.**
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prefix: "--format"
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```
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<a name="recordinputs"></a>
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## Record Inputs 📀
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## How do I describe dependent or exclusive input parameters(e.g. How do I use record inputs)?
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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.
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inputBinding:
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prefix: "--chromosomes"
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```
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## Setting Mutually Exclusive Parameters
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## How do I set mutually exclusive parameters?
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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.
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out: [indexes]
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```
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## Setting Booleans
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## How can I set Booleans?
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These can be set by using the default field
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```yaml
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input:
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default:true
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```
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## Concatenating Strings in Inputs
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## What should I do when concatenating strings in inputs?
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The valueFrom field must be used instead of default.
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My String: $(input.stringvalue)
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```
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## `cwltool` Errors due to Filenames with Space Characters Inside
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## I get `cwltool` errors due to filenames with space characters inside. What should I do?
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`cwltool` does not allow some characters in filenames by default.
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If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`.
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## CWL Parameter Reference Error due to Hyphen in Input Identifier
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## What should I do when I get CWL Parameter Reference error due to hyphen in an input identifier?
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If `cwltool --validate` returns valid
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valueFrom: $(inputs["sample-input"])
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```
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## Use CWL and cwltool with Singularity
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## How do I use CWL and cwltool with Singularity?
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The CWL standards are built around (optional) Docker format containers.
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The reference runner and several other CWL implementations support running
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those Docker format containers using the Singularity engine. Directly
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specifying a Singularity format container is not part of the CWL standards.
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## Debug JavaScript Expressions
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## How do I debug the JavaScript in my CWL tool?
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You can use the <code>--js-console</code> option of <code>cwltool</code>, or you can try
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creating a JavaScript or TypeScript project for your code, and load it

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