cant_hyd_HMM_scores.tsv filename case mismatch in Globus database

[cduvallet]

Description of the bug

Running DRAM2 with --anno_dbs including canthyd fails with Error: Invalid value for '--hmm_info_path': Path 'cant_hyd_HMM_scores.tsv' does not exist. The file is present in databases/canthyd/hmm/, but named CANT_HYD_HMM_scores.tsv (all caps) rather than the lowercase cant_hyd_HMM_scores.tsv. Filesystem is case-sensitive (Linux), so these are treated as different files.

Workaround: symlinking to the expected name fixes it:

ln -s databases/canthyd/hmm/CANT_HYD_HMM_scores.tsv databases/canthyd/hmm/cant_hyd_HMM_scores.tsv

System information

• DRAM version: DRAMv2, 2.0.0-beta28, dev branch, revision e7fa28b
• Nextflow version: 26.04.6
• Hardware: Cloud (AWS EC2, r6i.8xlarge)
• Executor: local
• Container engine: Docker (Docker Engine 29.1.3)
• OS: Ubuntu 26.04 LTS, x86_64

Command used and terminal output

nextflow run WrightonLabCSU/DRAM -r dev --input_fasta input_fasta --outdir results_full --rename --call --annotate --anno_dbs dram_db,kofam,camper,canthyd,dbcan,fegenie,merops,methyl,sulfur,metals,antismash,card,tcdb,vog,viral --tiny_gb_mem_limit 4 -profile docker -resume

Terminal output:
Error: Invalid value for '--hmm_info_path': Path 'cant_hyd_HMM_scores.tsv' does not exist.

Container:
  community.wave.seqera.io/library/python_pandas_polars_hmmer_pruned:6d5bc9dfeca29b70

Relevant files

No response