template: dollar variables in sh script (awk, $1, $2)

[Damian Loska]

Hey, I have some template script, "test.sh", with a simple line:

zgrep -v "#" $vcfgz  | awk '{print $1}'

However running it from NF

    script:
        template "test.sh"

gives error:

Error executing process > 'test (1)'

Caused by:
  Failed to parse template script (your template may contain an error or be trying to use expressions not currently supported): org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/groovy/script/Script58F540A7305FFF8AA14EBC89E87E23F4: 3: token recognition error at: '1' @ line 3, column 28.
   zcat $vcfgz | awk '{print $1}'""");


1 error

So the problems are "dollar" references in the .sh script. Can I somehow omit it? 

Ideally I'd need optional input arguments to the test.sh script:

if it's run standalone, I'd like to run:
bash test.sh firstParamter

and if it's run from NF I'd use only:

template "test.sh" (no need parameters)

Thanks
Damian

[Alan Hoyle]

Try \$1

-- 

- Alan Hoyle -  al...@alanhoyle.com - https://www.alanhoyle.com/  -

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Subject: template: dollar variables in sh script (awk, $1, $2)

 

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[Damian Loska]

\$1 doesn't work when I run the script standalone (i,e: bash test.sh firstParam)

I want to easily use the script both from the nextflow, as well as a standalone run

[Sam]

You can find the related documentation here:

https://www.nextflow.io/docs/latest/process.html?highlight=template

Might need an input val(vcfgz)

[Alan Hoyle]

Maybe Use the shell block documented here:

https://www.nextflow.io/docs/latest/process.html

that makes your nextflow processes use !{varname} and lets you use ${bash_var_name} 

--
  -  Alan Hoyle  -  al...@alanhoyle.com  -  http://www.alanhoyle.com/  -

[Damian Loska]

Well, your answers are helpful, but partially correct:)

What I needed to do is:

process test {
    echo true
    shell:
        template "my_script.sh"
}

instead of:

process test {
    echo true
    script:
        template "my_script.sh"
}

my_script.sh contains simple:
echo "uuu bbbb" | awk '{print $1}'

THANKS!
DL