Hello, how do we provide/download the dbs for Foldseek? According to the Foldseek README,

foldseek databases

will download the dbs, so I expected to be able to provide the name

Alphafold/Swiss-Prot

and it would download it. Here’s what I see in the visual config on Seqera (attached). I see that Foldseek databases are available here: https://foldseek.steineggerlab.workers.dev/ — but I’d really rather the pipeline take care of downloading the potentially 100s of GB-sized files. Here’s my output log:

Workflow execution completed unsuccessfully
The workflow execution failed to start. Exit status: 1

Essential container in task exited
Nextflow 24.10.5 is available - Please consider updating your version to it
N E X T F L O W  ~  version 24.10.4
Pulling nf-core/proteinfold ...
downloaded from <https://github.com/nf-core/proteinfold.git>
Launching `<https://github.com/nf-core/proteinfold>` [backstabbing_lavoisier] DSL2 - revision: 8e0384e355 [dev]
Downloading plugin nf-schema@2.3.0
------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/proteinfold 1.2.0dev
------------------------------------------------------
Global options
  input                           : <s3://REDACTED/samplesheet.csv>
  outdir                          : <s3://REDACTED/proteinfold/2025-03-30-dev/>
  use_gpu                         : true
  split_fasta                     : true
  email                           : olga@seanome.org
Foldseek options
  foldseek_search                 : easysearch
  foldseek_db                     : Alphafold/Swiss-Prot
Colabfold DBs and parameters links options
  colabfold_alphafold2_params_path: null/params/alphafold_params_2021-07-14
  colabfold_alphafold2_params_tags: {alphafold2_multimer_v1=alphafold_params_colab_2021-10-27, alphafold2_multimer_v2=alphafold_params_colab_2022-03-02, alphafold2_multimer_v3=alphafold_params_colab_2022-12-06, alphafold2_ptm=alphafold_params_2021-07-14}
Generic options
  trace_report_suffix             : 2025-03-30_21-47-28
Core Nextflow options
  revision                        : dev
  runName                         : backstabbing_lavoisier
  launchDir                       : /
  workDir                         : /REDACTED/scratch/24wHCtFKxblxSj
  projectDir                      : /.nextflow/assets/nf-core/proteinfold
  userName                        : root
  profile                         : standard
  configFiles                     : /.nextflow/assets/nf-core/proteinfold/nextflow.config, /nextflow.config
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    <https://doi.org/10.5281/zenodo.7629996>
* The nf-core framework
    <https://doi.org/10.1038/s41587-020-0439-x>
* Software dependencies
    <https://github.com/nf-core/proteinfold/blob/master/CITATIONS.md>
ERROR ~ Argument of `file` function cannot be null
-- Check script '.nextflow/assets/nf-core/proteinfold/main.nf' at line: 332 or see 'nf-24wHCtFKxblxSj.log' file for more details

Edit: Updated missing part of output log

Hi, I am afraid the pipeline does not download this DB at the current stage, so you will need to download the DBs outside of the pipeline. Pin @Ziad Al-Bkhetan as he implemented this part in case he could be more helpful

Implementing it for a future release would be great. Keiran recommends using the Steinnegger mirror as the other mirror is unusably slow: https://foldseek.steineggerlab.workers.dev/

Unfortunately, I have not implemented the DB download in the pipeline for foldseek 😞. Maybe something we can work on soon.

Issue opened here: https://github.com/nf-core/proteinfold/issues/288