"NFCORE_CIRCRNA:CIRCRNA:BSJ_DETECTION:COMBINEBEDS_READS": AttributeError: 'Index' object has no attribute 'levels'.

### 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 <module> 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](https://github.com/user-attachments/files/20442611/nextflow.log) ### Command used and terminal output ```console # 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](https://github.com/user-attachments/files/20442691/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)