Output the theoretical .command.sh file when using stub

[awgymer]

It would be great if there was a way to run a workflow with -stub but also get the result of what would have run in the script section.

Currently I have a work around that looks something like this:

script:
def prefix = task.ext.prefix ?: "${meta.id}"
def args = teask.ext.args ?: ""
"""
some command \
    $input \
    $args 
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def args = teask.ext.args ?: ""
command = """
some command \
    $input \
    $args 
"""

"""
echo '${command}'

touch myoutput.txt
"""

But obviously this creates a lot of code duplication and requires one to carefully keep the stub section aligned with every chaneg to the script section.

Suggest implementation

Could be default to output the would-be script to .command.sh.stub or something.
Or it could be an additional option like --stub-run-verbose or some such.
I am not sure how easy this would be to implement with how nextflow is written in honesty.

[warrenson]

But obviously this creates a lot of code duplication...

This is why I am here now.

Another suggestion

I'd be happy if the script text was available in the $task map when running in stub mode. So you could include it in the stub like:

stub:
echo "$task.script"
touch some output

Which would print the script contents, with variables expanded, in the .command.sh on the stub output.

(I edited this comment to add the suggestion)