Update Nextflow workflows: GPU support, new processes, improved auto-detection#93
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FIrgolitsch wants to merge 5 commits intomainfrom
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Update Nextflow workflows: GPU support, new processes, improved auto-detection#93FIrgolitsch wants to merge 5 commits intomainfrom
FIrgolitsch wants to merge 5 commits intomainfrom
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soct_3d_reconst.nf: adds GPU process management, shift analysis with outlier filtering, mask creation, slice quality assessment, interpolation for missing slices, pipeline report generation, improved mosaic grid auto-detection, and CPU thread limiting. Corresponding nextflow.config updates for GPU parallelism, new process configurations, and new parameter groups (galvo, resolution, missing-slice interpolation). preproc_rawtiles.nf and its config gain GPU options for preprocessing.
…ndle encoder glitch spikes, enhancing robustness of common space alignment.
…fov_mm parameter for artifact correction and refining unreliable shifts using image registration.
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Closing in favour of #102 (recreated with squashed commits as part of the PR split plan refresh). |
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Summary
Updates both Nextflow workflows to integrate all the new capabilities introduced in the preceding PRs (PRs #85–#92).
workflows/reconst_3d/soct_3d_reconst.nfLINUMPY_MAX_CPUSworkflows/reconst_3d/nextflow.configworkflows/preproc/preproc_rawtiles.nf+nextflow.configDependencies
Depends on all preceding PRs (#85–#92).