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Shell command requirement #329

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Shell command requirement #329

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a629e13
edit hd5 to hdf5 and fix broken link
Fienne Oct 20, 2022
647240d
include shell command requirement in FAQ
Fienne Oct 21, 2022
d4da617
define shell command requirement
Fienne Oct 24, 2022
bfca842
update shell command requirement
Fienne Oct 24, 2022
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Merge branch 'main' into shell-command-requirement
tetron Oct 24, 2022
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Merge branch 'main' into shell-command-requirement
tetron Oct 24, 2022
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10 changes: 10 additions & 0 deletions src/faq.md
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Expand Up @@ -446,6 +446,16 @@ 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.

## Shell Command Requirement
`ShellCommandRequirement` in CWL is used to convert a list of arguments into a string containing a shell command line.
Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent intepretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`.
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If you're going to copy text from the specification, you have to at least reword it so it is speaking to the right audience.

The specification is speaking to people who are writing code to run CWL. So when it says "it must do something" it is saying their CWL runner must do this.

For the audience of CWL users, you want to say what will happen. So this needs to be change to say "...each item will be joined..."


If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes.
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Needs example.

`ShellCommandRequirement` in CWL allows us to use `/bin/sh -c` in order to pass our command as a string to a shell intrepreter. `ShellQuote:false` leaves shell metacharacters unquoted, and thus they can still be interpreted and used by a shell.

To use the `ShellCommandRequirement`, you need to pass in the class name `ShellCommandRequirement` as a string.
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Needs example.



## Debug JavaScript expressions

You can use the <code>--js-console</code> option of <code>cwltool</code>, or you can try
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