Add newlines and set command to fix #3416

[mahesh-panchal]

Fixes the fix to template #3416.

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• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[ewels]

Please don't merge this until we confirm that it isn't a problem on the Nextflow side.

I think that process.shell is used in more places than just the header of .command.sh which is how we got here in the first place, as it broke in .command.run. So multi-line commands can be problematic.

[ewels]

Yeah, I think today's Nextflow PR will trigger a failure if we merge this PR. See here:

if( !it || it.contains('\n') || it.contains('\r') )
    throw new IllegalArgumentException("Directive `process.shell` cannot contain new-line characters - offending value: ${shell}")

[mahesh-panchal]

The alternative is to modify the modules template to set these flags and a mass nf-core modules update to insert the flags. And then remove the flags from the shebang.

[ewels]

I think that there should be a better way. I think even setting process.shell back to /usr/bash would be preferable tbh.

Lots in play at the moment, see also nextflow-io/nextflow#5684

[mahesh-panchal]

Closing as the old method actually works, and I made a mistake in testing.