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…atch On AWS Batch, input validation occurs before ext.when can skip process execution. This caused "Path value cannot be null" errors when params.cellpose_model (default []) was passed to CELLPOSE even though ext.when would have skipped the process. Wrap each segmentation process (DEEPCELL_MESMER, CELLPOSE, MCCELLPOSE) in conditionals that check params.segmentation, ensuring processes are only invoked when actually needed. Fixes: #140 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
adamjtaylor
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AlexBarbera and
jmuhlich
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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: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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…CELL_MESMER processes
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This pull request updates the segmentation workflow in
workflows/mcmicro.nfand related configuration to improve conditional execution and input handling for segmenters, particularly on AWS Batch. The changes ensure that each segmenter is only invoked when specified, preventing input validation errors and enhancing flexibility. Key updates also include improvements to how model files are staged and arguments are passed to segmenter processes.Workflow improvements for segmentation:
mesmer,cellpose,mccellpose) based onparams.segmentation, preventing input validation errors when segmenters are skipped. This is especially important for AWS Batch compatibility. [1] [2]cellposesegmenter logic to use explicit channels for images and models, with improved handling of the model file (checks existence and supports empty value).Process and configuration enhancements:
CELLPOSEprocess to use thestageAsoption for the model input, allowing flexible file staging.MCCELLPOSEprocess viaext.argsin the configuration.