Convert sentieon modules to topics and update version #9700
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Wrap environment variables in env() function to comply with Nextflow
strict syntax mode (NXF_SYNTAX_PARSER=v2). This addresses 58 lint errors
across Sentieon and Spotiflow module test configs.
Changes:
- Sentieon modules: Replace ${SENTIEON_LICSRVR_IP} with ${env('SENTIEON_LICSRVR_IP')}
- Sentieon modules: Replace ${SENTIEON_AUTH_MECH} with ${env('SENTIEON_AUTH_MECH')}
- Spotiflow module: Replace ${HOME} with ${env('HOME')}
This is part of the migration to Nextflow strict syntax where implicit
environment variable references are not allowed.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
SPPearce
changed the title
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@nf-core-bot fix linting |
maxulysse
approved these changes
Jan 21, 2026
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Converting a number of the sentieon modules to emit a versions.yml.
Also doing some housekeeping (modules_args, fixing broken tests) and swapping to the most recent sentieon version.
This isn't all the submodules, but figure I should stop to make it manageable