Description of the bug

Dear nf-core/circRNA team,

I am currently trying to run the nf-core/circRNA pipeline but it gets stuck at the following step: "NFCORE_CIRCRNA:CIRCRNA:BSJ_DETECTION:COMBINEBEDS_READS"

Here is the .command.err output since .command.out is empty:
INFO: underlay of /etc/localtime required more than 50 (74) bind mounts
mkdir -p failed for path /home/.config/matplotlib: [Errno 30] Read-only file system: '/home/.config'
Matplotlib created a temporary cache directory at /gpfs/data/tmp/matplotlib-uwf72cul because there was an issue with the default path (/home/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Traceback (most recent call last):
File "/gpfs/data/nxt_work/circRNA/b1/72726b3a4a338e67cce32a0528f272/.command.sh", line 43, in
bsj_upset = UpSet(bsj_upset_data, show_counts=True, subset_size="count")
File "/opt/conda/lib/python3.13/site-packages/upsetplot/plotting.py", line 343, in init
(self.total, self._df, self.intersections, self.totals) = _process_data(
~~~~~~~~~~~~~^
data,
^^^^^
...<10 lines>...
include_empty_subsets=include_empty_subsets,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/opt/conda/lib/python3.13/site-packages/upsetplot/plotting.py", line 37, in _process_data
results = query(
df,
...<9 lines>...
include_empty_subsets=include_empty_subsets,
)
File "/opt/conda/lib/python3.13/site-packages/upsetplot/reformat.py", line 369, in query
data = _check_index(data)
File "/opt/conda/lib/python3.13/site-packages/upsetplot/reformat.py", line 71, in _check_index
if not all({True, False} >= set(level) for level in df.index.levels):
^^^^^^^^^^^^^^^
AttributeError: 'Index' object has no attribute 'levels'. Did you mean: 'nlevels'?

The content of .command.sh seems to be the same as this one: https://github.com/nf-core/circrna/blob/dev/modules/local/combinebeds/reads/templates/reads.py

Could someone please point me in the right direction for troubleshooting this issue? Could this be a Python package syntax problem, where the function is named differently in different versions?

Thank you for any tip and suggestion!
Best,
pnolabs

nextflow.log

Command used and terminal output

# Run nextflow pipeline with test profile
nextflow run nf-core/circrna -r dev \
    -profile singularity \
    -resume \
    -c /gpfs/data/.../scripts/circRNA/nxt.config \
    -params-file /gpfs/data/.../scripts/circRNA/params.yml \
    --input /gpfs/data/.../01_data/circRNA/samplesheet.csv \
    --outdir /gpfs/data/.../02_analysis/circRNA/output \
    --phenotype /gpfs/data/.../01_data/circRNA/phenotype.csv

Relevant files

params.txt

System information

Nextflow version 24.10.3
Hardware HPC
Executor slurm
Container engine: Singularity 3.8.7
OS AlmaLinux release 8.8 (Sapphire Caracal)
Version of nf-core/circrna (dev)