Experimental feature to change substitution prefix.

[tetron]

Example of combining this feature with attachments (common-workflow-language/schema_salad#254) to simplify wrapping an inline bash script:

#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool $namespaces: cwltool: "http://commonwl.org/cwltool#" baseCommand: [/bin/sh, script] requirements: cwltool:SubstitutionPrefix: substitutionPrefix: "@" InitialWorkDirRequirement: listing: - entryname: script entry: {$include: "#attachment-1"} inputs: msg: string outputs: output: type: File outputBinding: glob: output.txt --- | echo Zip@(inputs.msg) $(date) > output.txt 

[mr-c]

For your example I would demonstrate use of EnvVarRequirement and turn off the substitution altogether

[multimeric]

I like it. I think having this would solve a lot of issues.

However I still believe InitialWorkDirRequirement is not the most logical place for the inclusion of scripts. We still need a construct that is intuitively for including scripts and setting them as the tool's command, which is where my ScriptTool proposal etc come in. That said we could reasonably add this substitutionPrefix feature in independently from any better mechanism for referring to scripts.