RoseTTAFold-All-Atom errors out despite completing structure prediction

[jscgh]

Description of the bug

Nextflow fails due to t000_.ss2 not being available for cat and being unable to cp 7u7w_A.pdb (RFAA produced filename is 7u7w.pdb). This is caused by proteinfold and hydra (RFAA) having different ways of handling naming.

.command.err:

- 13:40:45.730 INFO: Input file = 7u7w/A/hhblits/t000_.1e-10.a3m
- 13:40:45.730 INFO: Output file = 7u7w/A/hhblits/t000_.1e-10.id90cov75.a3m
- 13:40:45.893 WARNING: Maximum number 100000 of sequences exceeded in file 7u7w/A/hhblits/t000_.1e-10.a3m
- 13:41:09.503 INFO: Input file = 7u7w/A/hhblits/t000_.1e-10.a3m
- 13:41:09.503 INFO: Output file = 7u7w/A/hhblits/t000_.1e-10.id90cov50.a3m
- 13:41:09.659 WARNING: Maximum number 100000 of sequences exceeded in file 7u7w/A/hhblits/t000_.1e-10.a3m
cat: 7u7w/A/t000_.ss2: No such file or directory
cp: cannot stat '7u7w_A.pdb': No such file or directory

Command used

module load nextflow/24.04.4 java/21                                                                  export SINGULARITY_CACHE_DIR=/srv/scratch/sbf/singularity_cache                                       export NXF_SINGULARITY_CACHEDIR=/srv/scratch/sbf/singularity_cache                                                                                                                                          nextflow run /srv/scratch/z5378336/proteinfold/main.nf \                                                  --input 7u7w_A.csv \                                                                                  --outdir output \                                                                                     --mode rosettafold_all_atom \
    --rosettafold_all_atom_db /mnt/af2 \
    --alphafold2_db /mnt/af2 \
    --use_gpu \
    --skip_multiqc \
    -resume \
    -profile apptainer

For

#17
nf-core#197