CODE chunk

[Liripo]

workflow test {
	String workdir="/path/to/outdir"
	call test_do {
		input:
			workdir=workdir
	}
}

task test_do {
	String workdir
	command <<<
		cd ${workdir}
		echo "start" >log
		R <<CODE
			readr::write_lines(mtcars$am,"a.txt")
		CODE
		echo "end">>log
	>>>
}

while i run this code,the $am is parsed as a shell variable,Is this a bug or is it designed like this?
I am using cromwell to run wdl.

[DavyCats]

This sounds like more of a bash issue, $am isn't a WDL placeholder, so I don't think a WDL execution engine would be doing anything with it.

As a side note, it seems you're using WDL draft-2, I would recommend using WDL 1.0 if possible (or even 1.1, except that cromwell doesn't support it yet).

[Liripo]

I will try WDL1.1 if I have a chance

[pshapiro4broad]

This a feature of bash heredocs. If you want to prevent substitution, quoting the $ could work, or you could use a heredoc form that doesn't do substitution: <<'. See https://tldp.org/LDP/abs/html/here-docs.html

[Liripo]

Thank you