Fix environment variable references for strict syntax compliance

[ewels]

Wraps environment variable references in env() function for strict syntax compliance.

Details

Changes

This PR fixes 58 strict syntax errors across 30 files by wrapping environment variable references in the env() function, as required by Nextflow 25.10+ strict syntax mode.

Example fix:

// Before
${SENTIEON_LICSRVR_IP}

// After
${env('SENTIEON_LICSRVR_IP')}

Why

Nextflow 25.10 introduces strict syntax mode (enabled via export NXF_SYNTAX_PARSER=v2) which will become mandatory in future versions. In strict mode, environment variables must be accessed explicitly using the env() function rather than directly by name.

Affected Files

• Sentieon modules (30 files)
• Spotiflow test configs

Testing

• All changes maintain backward compatibility with non-strict mode
• Pre-commit hooks passed (prettier, whitespace checks)
• Ready for nextflow lint validation

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This work was completed with AI assistance using Seqera AI.

[mashehu]

I guess there should also be several $TMPDIR with the same problem

[ewels]

Ok, it looks like env() is not backwards compatible to the old language parser, so I can't make this change without breaking backwards compatibility (which I've been trying to avoid with the strict syntax fixes).

I'll use the old-style System.getenv() instead of env() for now and drop in some comments that when we bump the minimum Nextflow version to 26.04.0 where strict syntax is on by default (eg. by updating to the new process input syntax) , that they should be updated.

Update: I was wrong about this. Added env() back in #9732

[ewels]

@maxulysse @FriederikeHanssen I was assuming that the tests were failing because of something I did, but is it possible that the Senteion tests are failing because of an unrelated error? It's to do with fetching the licence file.

[maxulysse]

@maxulysse @FriederikeHanssen I was assuming that the tests were failing because of something I did, but is it possible that the Senteion tests are failing because of an unrelated error? It's to do with fetching the licence file.

@edmundmiller ?

[SPPearce]

Sentieon tests only run when ran from the nf-core organisation, so you need to make the branch there, not your own fork.

[ewels]

d'oh! Of course.. I'll remake this PR from a branch.

[ewels]

See #9708

[SPPearce]

Closing this one then