Registration glitch in s3 resolution

## Bug report ## Description of the problem I tried to register 2-round data using `def_scale=s3` and `aff_scale=s4`. The pipeline ran almost through, but errored out at `Error executing process > 'registration:final_transform (4)`. This error can be reproduced using `demo_medium` data with `def_scale=s3`. Upon checking, I believe this is because of a glitch: the default scale `s2` is still hard coded somewhere in the process (see error message below), causing inconsistencies. Does this make sense and could you help me resolve this? Thanks so much! ## Log file(s) ``` May-29 22:24:58.258 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'registration:final_transform (4)' Caused by: Process `registration:final_transform (4)` terminated with an error exit status (1) Command executed: echo "Final transform" # Must remove the output directory, or we get a zarr.errors.ContainsArrayError if it already exists rm -rf /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/registration/LHA3_R5_medium-to-LHA3_R3_medium/warped/c3/s3 || true umask 0002 /app/scripts/waitforpaths.sh /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R3_medium/stitching/export.n5/c3/s3 /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/stitching/export.n5/c3/s3 /entrypoint.sh apply_transform_n5 /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R3_medium/stitching/export.n5 /c3/s3 /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/stitching/export.n5 /c3/s3 /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/registration/LHA3_R5_medium-to-LHA3_R3_medium/transform /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/registration/LHA3_R5_medium-to-LHA3_R3_medium/warped echo "Finished final transform for /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/registration/LHA3_R5_medium-to-LHA3_R3_medium/warped/c3/s3" Command exit status: 1 Command output: Final transform Checking for /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R3_medium/stitching/export.n5/c3/s3 Checking for /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/stitching/export.n5/c3/s3 Command error: INFO: Could not find any nv files on this host! INFO: Converting SIF file to temporary sandbox... Final transform Checking for /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R3_medium/stitching/export.n5/c3/s3 Checking for /u/scratch/f/f7xiesnm/demo_medium_v2/outputs/LHA3_R5_medium/stitching/export.n5/c3/s3 Traceback (most recent call last): File "/app/bigstream/apply_transform_n5.py", line 73, in <module> grid = read_n5_transform(txm_path, '/s2') File "/app/bigstream/apply_transform_n5.py", line 42, in read_n5_transform grid = txm_n5['/c0'+subpath].shape[::-1] File "/opt/conda/envs/myenv/lib/python3.8/site-packages/zarr/hierarchy.py", line 349, in __getitem__ raise KeyError(item) KeyError: '/c0/s2' ``` ### Environment * EASI-FISH Pipeline version: this May * Nextflow version: 22.10.07 * Container runtime: Singularity * Platform: Local * Operating system: Linux ### Additional context No.