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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>
mashehu
approved these changes
Jan 22, 2026
cavenel
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to cavenel/modules
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this pull request
Feb 5, 2026
* Fix environment variable references for strict syntax compliance
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>
* Use System.getenv() for backwards compatability
* Update sentieon/bwamem to topic
* Add bwa version back
* Fix linting
* Swap environment.yml to new version
* Use nft-bam
* Use nft-bam
* Update all sentieon modules
* Fix some modules
* Prettier
* Add missing variable from stub
* Update qualcal
* Update varcal
* More updates
* Fix singularity container for wgsmetrics and conda versions
* Fix some undefined it warnings
* Update snapshot
* Remove trailing spaces
* Fix wgsmetrics linting
* Fix dedup
* Fix sentieon/dedup
* Update more modules
* Update more modules
* Bump all modules to 202503.02
* Update snapshots
* Update datametrics and rsem
* Update rsem
* Use correct version
* Update datametrics
---------
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
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