This repository has been archived by the owner on Apr 10, 2023. It is now read-only.

Layout of files

This is probably a bit too rigid, but it works for us at the moment. If we plan to scale things up it may be worth properly thinking things through.

slide1
- scene1
  - tiles
    - round1
      - 0.ome.tiff
      - ...
    - round2
      - 0.ome.tiff
  - image.ome.tiff
  - image.ome.zarr
- scene2
  - ...
- .brightfield
- .illumination
  - flatfield-{round}.tiff
  - darkfield-{round}.tiff
- .scan-logs
- .logs
  - nextflow
    - before-annotate.log
    - before-annotate.report.html
    - before-annotate.trace.txt
    - before-annotate.timeline.html
    - after-annotate.log
    - after-annotate.report.html
    - after-annotate.trace.txt
    - after-annotate.timeline.html
  - illum-profiles
    - make-illum-profiles-{round}.dask-performance.html
    - plot-illum-profiles-{round}.svg
  - stack-tiles
    - stack-tiles-{round}-{scene}.dask-performance.html
  - unmixing-mosaics
    - make-unmixing-mosaic-{round}.dask-performance.html
  - segmentation
    - segment-{scene}.dask-performance.html
calibration-dir
- cube-alignment
  - gifs
  - images
  - plots
  - scales-shifts
  - .logs
    - cube-alignment-{timestamp}.dask-performance.html
- dark
- lamp
- stage-xy

Nextflow notes

for conda to specify certain functions as entry points, the filenames of the files containing said functions must be importable (e.g. no dashes in filename)