I have to pass an environment variable to my tool to keep Java behaving well (avoid writing a particular file to /tmp which causes collisions under some Apptainer configurations), unfortunately this includes when passing

--version

. With

versions.yml

I could

export

this early in the

script:

block which gets picked up by both the actual tool invocation and the

--version

invocation. But with topic channels it looks like I need to stick this in the

eval

qualifier and thus also in the meta.yml block. This looks kind of horrendous. Is there a better way to handle this? Here's the command line I'm currently using:

JAVA_TOOL_OPTIONS='-XX:+PerfDisableSharedMem' ashlar --version | sed 's/^.*ashlar //'

This leads to the following in `meta.yml`:

versions_ashlar:
    ...
    - JAVA_TOOL_OPTIONS='-XX:+PerfDisableSharedMem' ashlar --version | sed 's/^.*ashlar //':
        type: eval
        description: The expression to obtain the version of the tool

(I also note that

nf-core modules lint --fix

wrapped that line in the generated output which caused a yaml syntax error "ScannerError: mapping values are not allowed here", crashing

nf-core

!)