Issue in test run with conda

[OlivierCoen]

Description of the bug

When running the pipeline with the test profile, I get issues.

Command used and terminal output

I ran the following command:

nextflow run nf-core/hic \
   -profile conda,test \
   -c custom.config \
   -resume

where custom.config is:

executor {
    cpus = 12
    memory = 100.GB
}

I get:

ERROR ~ Error executing process > 'NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})'

Caused by:
  Process `NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})` terminated with an error exit status (1)


Command executed:

  cooler makebins \
       \
      W303_SGD_2015_JRIU00000000.fsa.sizes \
      1000 > cooler_bins_1000.bed
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS":
      cooler: $(cooler --version 2>&1 | sed 's/cooler, version //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/coen/nfcore_hic/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/bin/cooler", line 6, in <module>
      from cooler.cli import cli
    File "/home/coen/nfcore_hic/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/__init__.py", line 14, in <module>
      from .api import Cooler, annotate
    File "/home/coen/nfcore_hic/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/api.py", line 13, in <module>
      from .core import (
    File "/home/coen/nfcore_hic/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/core.py", line 3, in <module>
      from pandas.api.types import is_categorical
  ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/home/coen/nfcore_hic/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/pandas/api/types/__init__.py)

Work dir:
  /home/coen/nfcore_hic/work/6f/1296a4a7f9bedf2ca7b814945afcd4

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

I tried to run it with apptainer because I'm on a multi-user environment and I cannot use docker, but I have another issue when running the pipeline with apptainer (which is another issue and is related to the nf-core framework in general, so it's not relevant here).

System information

OS: Ubuntu 24.04.4
conda: 26.1.1

Thanks a lot!