[Internal] [Bug] User config plugins will be ignored: [email protected] and invalid input values

[jessicarowell]

Description.
WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: [email protected]
WARN: The following invalid input values have been detected:

• --lift_unmapped_features_file_name: output.unmapped_features.txt

Run environment (container, cloud service, HPC, platform, etc.)
SciComp, not HPC

Command to replicate the error:
nextflow run main.nf -profile test,singularity --species rsv --annotation false --submission true --sra true --genbank false --biosample true --output_dir test_rsv --submission_config ~/02.scratch/submission_config.yaml --meta_path /scicomp/home-pure/ick4/01.scripts/tostadas/assets/sample_metadata/onehealth_biosample_package_template.xlsx --custom_fields_file /scicomp/home-pure/ick4/01.scripts/tostadas/assets/custom_meta_fields/onehealth_biosample_pkg.json --validate_custom_fields true

Any Additional Context or Information?

[jessicarowell]

This warning occurs in Nextflow version 24.04.2 (default on nettie server), but not on 23.10.0 (default on biolinux).

Ramiya found this thread indicating a change in Nextflow defaults ("all" vs. "dist") changed the number of core plugins. Seems the solution with be to use nextflow plugin install <pluginId,..> from this NF docs page and indicate that in README.