proteinfold DB paths not being resolved properly

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.

May 31 '23 11:05 drpatelh

Should be fixed in the next NF edge release: https://github.com/nextflow-io/nextflow/issues/4081

For now, it may be worth trying NF 23.04.2.

Jul 31 '23 13:07 drpatelh

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

Apr 05 '24 13:04 JoseEspinosa

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

Apr 18 '24 08:04 JoseEspinosa

This should be addressed in dev now and will be made available in v1.1.0, thus will close the issue

Jun 21 '24 13:06 JoseEspinosa