Description of the bug

Normal run of the pipeline leads to the following error
Process NFCORE_MHCQUANT:MHCQUANT:PYOPENMS_IONANNOTATOR input file name collision -- There are multiple input files for each of the following file names

Command used and terminal output

nextflow run nf-core/mhcquant -r dev -profile cfc --input  --outdir ./results --fasta --digest_mass_range 800:2500 --activation_method CID --prec_charge 2:3 --fdr_threshold 0.05 --number_mods 3 --precursor_mass_tolerance 5 --fragment_mass_tolerance 0.02 --num_hits 1 --peptide_min_length 8 --peptide_max_length 12 --max_rt_alignment_shift 300 --max_time '240.h' --email marissa.dubbelaar@uni-tuebingen.d

Relevant files

No response

System information

• Nextflow version: 22.04.4
• Hardware: HPC
• Container engine: Singularity
• Version of nf-core/mhcquant: dev