PRELOADKRAKENUNIQ: Minor fix following #8397 #8483
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params.krakenuniq_ram_chunk_size. Pass ram_chunk_size to database preload call and each classify call.
Krakenuniq command-line option `--preload-size` is non-mandatory. When it is required, it should be passed in `ext.args`. Also, remove the associated process input, `ram_chunk_size`.
When `--preload-size` option is passed in `ext.args`, preloading the database is not necessary and may unnecessarily consume memory.
Remove input `ram_chunk_size`. Pass `--preload-size $ram_chunk_size` in `ext.args` to load database in chunks. Database will be loaded into memory prior to classification if and only if option `--preload-size` is not present in `ext.args`.
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Jun 3, 2025
* Pass task.ext.args last to give them precedence over params.krakenuniq_ram_chunk_size. Pass ram_chunk_size to database preload call and each classify call. * Remove krakenuniq command-line option `--preload-size`. Krakenuniq command-line option `--preload-size` is non-mandatory. When it is required, it should be passed in `ext.args`. Also, remove the associated process input, `ram_chunk_size`. * Preload database if and only if option `--preload-size` is not present. When `--preload-size` option is passed in `ext.args`, preloading the database is not necessary and may unnecessarily consume memory. * Fix bug in database preloading. Remove input `ram_chunk_size`. Remove input `ram_chunk_size`. Pass `--preload-size $ram_chunk_size` in `ext.args` to load database in chunks. Database will be loaded into memory prior to classification if and only if option `--preload-size` is not present in `ext.args`. * Reference `preload_cmd` in BASH script instead of concatenating scripts. * Use environment variable to control preloading of database. * Don't export variable. * Restructure preload insertion * Add test that preload works * Fix logic * Fix logic in stub block. --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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PR checklist
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile condaThis PR fixes minor problems in the stub block,
preload_cmddefinition:scriptblock.echo.