Supplying a directory to --gtdbk-db breaks GTDB-Tk

[jfy133]

Description of the bug

I think the error comes from the nf-core module itself, as it has path(database/*) that will try and unpack the whole contents and it in it's own directory. But if you supply a directory, what does into the database/ is the directory, not the contents.

This is why I believe the data preparation module in mag strips the directory when emitting

Command exit status:
  1

Command output:
  [2024-02-12 10:39:17] INFO: GTDB-Tk v2.3.2
  [2024-02-12 10:39:17] INFO: gtdbtk classify_wf --extension fa --genome_dir bins --prefix gtdbtk.MEGAHIT-MaxBin2-unclassified-unrefined-ERS6299593 --out_dir /shared/jamesyates/acad-workshop/work/88/f4ac26581de92717e84d177de767c5 --cpus 10 --skip_ani_screen --scratch_dir pplacer_tmp --min_perc_aa 10 --min_af 0.65
  
  ================================================================================
                                       ERROR                                      
  ________________________________________________________________________________
  
             The GTDB-Tk reference data does not exist or is corrupted.           
  GTDBTK_DATA_PATH=database
  
     Please compare the checksum to those provided in the download repository.    
            https://github.com/Ecogenomics/GTDBTk#gtdb-tk-reference-data          
  ================================================================================
  [2024-02-12 10:39:17] ERROR: Controlled exit resulting from early termination.

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  .command.sh: line 3: [: too many arguments

Work dir:
  /shared/jamesyates/acad-workshop/work/88/f4ac26581de92717e84d177de767c5

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Command used and terminal output

No response

Relevant files

No response

System information

No response

[jfy133]

Should be fixed (at least a sort of workfaround, still not happy with the module) here: #585