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Default use_whole_cell_only to true; hide mask smoothing and Cellpose preprocessing params - #47
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mikemcka merged 1 commit intoOct 8, 2026
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…llpose preprocessing params - use_whole_cell_only now defaults to true (config + schema default) - Mark every Mask smoothing and Cellpose preprocessing parameter as hidden in the schema, so they are not shown in the Seqera launch form or --help - Pin use_whole_cell_only = false in the cellmeasurement module test so its existing snapshot (which includes nuclear measurements) still applies - Document both changes in usage.md and CHANGELOG Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
use_whole_cell_onlynow defaults totrue(nextflow.configand schemadefault). Nuclei are no longer segmented or measured unless--use_whole_cell_only falseis set.smooth_masks,smooth_method,smooth_kernel_size,smooth_n_workers,smooth_chunksize,smooth_tolerance,smooth_min_area) and Cellpose preprocessing options (cellpose_tile_norm_blocksize,cellpose_clip_limit,cellpose_clahe_kernel_size,cellpose_gaussian_sigma) are marked"hidden": trueinnextflow_schema.json. They are not shown in the Seqera Platform launch form or in--help(shown with--show_hidden). They can still be set on the command line or in a params file. Their defaults are unchanged.modules/local/cellmeasurement/tests/main.nf.test: the basic test passes a nuclear mask, so it now setsuse_whole_cell_only = false. The existing snapshot still applies.docs/usage.mdandCHANGELOG.md(new Unreleased section) updated.Breaking change
Runs that do not set
use_whole_cell_onlyno longer produce nuclear masks or nuclear measurements. This includes theconf/test*profiles.Testing
nf-core pipelines schema lint nextflow_schema.json: schema valid, defaults matchnextflow.config. The only warning (kronos_allow_novel_defaults) predates this change.🤖 Generated with Claude Code