Run "warp_spots" only produced nothing

[FangmingXie]

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: nospots_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.

[neugun]

I think I also had this bug before, you need to run the warp_spots along with spot_extraction.