DB paths not being resolved properly

[drpatelh]

Description of the bug

When running without --alphafold2_db (default) all of the DB paths are printed as null/ in the Execution log on stdout. Looks like there is an issue in the way these paths need to be resolved. Used v1.0.0 of the pipeline.

params.yml

input: 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
outdir: 's3://<OUT_DIR>'
use_gpu: true

Will check to see if these databases are published where required to be re-used.

[drpatelh]

Should be fixed in the next NF edge release:
nextflow-io/nextflow#4081

For now, it may be worth trying NF 23.04.2.

[JoseEspinosa]

Also reported when running colabfold_webserver and not providing the --colabfold_db parameter, see this slack thread.

[JoseEspinosa]

The previous comment is a different bug; thus, I'll open a new issue for tracking it: #144.