Test config - panel field does not contains a valid key!

[Proton-NTA]

Description of the bug

When running the pipeline with the test data from the test-dataset and configuration of the test.config the following error occurs:

Container:
  quay.io/pixelgen-technologies/pixelator:0.22.1

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Dec-04 07:08:38.642 [Actor Thread 15] ERROR nextflow.Nextflow - Please check input samplesheet -> panel field does not contains a valid key!

Input: human-sc-immunology-spatial-proteomics
Valid options:
 -

### Command used and terminal output

```console
nextflow run 'https://github.com/nf-core/pixelator' -hub github -with-report 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/report.html' -with-timeline 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/timeline.html' -with-dag 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/dag.html' -with-trace 's3://report-test/pixelator/run-019ae82fc5697a989a9af30d3f7f8ab7/trace.tsv' -c nextflow-s3.config -c tower.config -c /vol/projects/clowm/nextflow.config -revision 1affbf6a29e608424038d17baf69cac37e2fa477 -params-file params.json

Relevant files

nextflow-debug-019ae82fc5697a989a9af30d3f7f8ab7.log

System information

Nextflow version: 25.10.0
Executor: slurm
Container engine: Docker
Version of nf-core/pixelator: 2.2.0

[johandahlberg]

Hi @Proton-NTA!

Thank you for reporting this issue. Could you try adding -profile docker to your command? I am not able to reproduce the error that your are seeing, but in the logs you sent I found this error:

...
    File "/usr/lib64/python3.12/site-packages/numba/core/caching.py", line 687, in __init__
      self._impl = self._impl_class(py_func)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/lib64/python3.12/site-packages/numba/core/caching.py", line 423, in __init__
      raise RuntimeError("cannot cache function %r: no locator available "
  RuntimeError: cannot cache function '_is_constant_csr_rows': no locator available for file '/usr/lib/python3.12/site-packages/scanpy/_utils/compute/is_constant.py'

That seems like it could be related to write permissions in the NUMBA_CACHE_DIR according to this github issue. When using the docker profile we set this explicitly to "NUMBA_CACHE_DIR": "/tmp/.numba_cache", so that might help.