feat: typed parameters - #1103
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Adds a statically typed `params` block generated with the VS Code Nextflow extension, plus manual corrections: - `help` is typed as `String?` so `--help <param>` keeps working (a bare `--help` resolves to the string "true", which utils_nfschema_plugin already special-cases). - optional parameters without a default get the `?` suffix. - file/directory parameters become `Path?`, which lets Nextflow do the existence check itself. `gtdb_db` and `checkm_download_url` stay `String` because their defaults are remote URLs that would then be resolved over the network on every run. - `metaeuk_mmseqs_db` stays `String` (it is a database name, not a path). - parameters whose defaults are configuration-dependent are declared without a default; nextflow.config keeps owning those values. - `deepmased_features_gzip` drops its redundant `= false`.
The typed `params` block in main.nf now owns the defaults. Only values that
other configuration files depend on are kept in nextflow.config: igenomes_base
and igenomes_ignore (read by conf/igenomes.config), the config_profile_* and
custom_config_* values, outdir, publish_dir_mode, monochrome_logs,
pipelines_testdata_base_path and trace_report_suffix.
conf/igenomes.config is converted from the nested `genomes { 'KEY' { ... } }`
syntax to a `params.genomes = ['KEY': [...]]` map literal, which is what the
v2 syntax parser accepts.
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.0.3. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
nf-core tools cannot yet read defaults from a typed `params` block, so it reports nextflow.config and the schema as out of sync. Both checks are disabled until tools catches up. `cli_typecast` is set to false because Nextflow now casts CLI parameters itself from the declared types; letting nf-schema cast them as well can trigger a StackOverflowError.
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❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
`ext.args` was a plain list, so it was evaluated while the config was being parsed. Now that min_contig_size has no default in nextflow.config, at that point the parameter is either null or the raw CLI string, and `params.min_contig_size < 1500` throws when a value is passed on the command line. Wrapping it in a closure defers evaluation until the typed parameters are resolved.
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).