Run "warp_spots" only produced nothing

## Bug report ## Description of the problem I tried to run `warp_spots` only using `main.nf` by skipping all other steps. The pipeline ran through with no error message, but it produced nothing: no`spots_cX_warped.txt` files were being produced. Do you know why is this and if/how I can fix it? Thanks! *Update: I used instead `main-warp-spots.nf` and got it to work. But the above bug is still there.* ## Log file(s) ``` acq_names : [r1, r2] channels : [c0, c1, c2, c3, c4] ref_acq : r1 steps_to_skip : [stitching, registration, segmentation, measure_intensities, spot_extraction, assign_spots] Jul-17 09:55:48.846 [main] DEBUG nextflow.Nextflow - Images to stitch: [] Jul-17 09:55:48.848 [main] DEBUG nextflow.Nextflow - Images for spot extraction: [] Jul-17 09:55:48.850 [main] DEBUG nextflow.Nextflow - Channels for spot detection: [c0, c1, c2, c4] Jul-17 09:55:48.850 [main] DEBUG nextflow.Nextflow - Images for segmentation: [] Jul-17 09:55:48.850 [main] DEBUG nextflow.Nextflow - Images to register: [] against [] Jul-17 09:55:48.850 [main] DEBUG nextflow.Nextflow - Images for warping spots: [r2] Jul-17 09:55:48.851 [main] DEBUG nextflow.Nextflow - Images for intensities measurement: [] Jul-17 09:55:48.851 [main] DEBUG nextflow.Nextflow - Images for assign spots: [] ... Jul-17 09:56:03.127 [Actor Thread 8] DEBUG nextflow.Nextflow - Existing spots file: [/u/home/f/f7xiesnm/project-zipursky/easifish/lt186/outputs/r2/stitching/export.n5, null, s0, /u/home/f/f7xiesnm/project-zipursky/easifish/lt186/outputs/r2/spots/spots_c4.txt] Jul-17 09:56:03.128 [Actor Thread 4] DEBUG nextflow.Nextflow - Extracted spots to warp: [/u/home/f/f7xiesnm/project-zipursky/easifish/lt186/outputs/r2/stitching/export.n5, null, /u/home/f/f7xiesnm/project-zipursky/easifish/lt186/outputs/r2/spots/spots_c4.txt] Jul-17 09:56:03.130 [main] DEBUG nextflow.Session - Session await > all processes finished Jul-17 09:56:03.200 [main] DEBUG nextflow.Session - Session await > all barriers passed Jul-17 09:56:03.209 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=2; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=16.5s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=2; peakMemory=2 GB; ] Jul-17 09:56:03.266 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Jul-17 09:56:03.529 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Jul-17 09:56:03.529 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye ``` ### Environment * EASI-FISH Pipeline version: ~ * Nextflow version: 22.10.7 * Container runtime: Singularity * Platform: Local * Operating system: Linux ### Additional context I have done `registration` and `spot_extraction` separately using the same pipeline, and have checked that both results look good.