--arg_rgi_db not working in v. 2.0.0

[amizeranschi]

Hi,

The parameter --arg_rgi_db doesn't seem to work as expected in v. 2.0.0 of the pipeline. The error looks like this:

Command error:
  Matplotlib created a temporary cache directory at /tmp/matplotlib-02ng_iet because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  mkdir: can't create directory 'card_database_processed': File exists

The following code should reproduce the error:

mkdir ~/test-funcscan-error
cd ~/test-funcscan-error

nextflow run nf-core/funcscan -r 2.0.0 \
-profile docker,test \
--run_amp_screening false \
--run_arg_screening \
--arg_skip_abricate \
--arg_skip_amrfinderplus \
--arg_skip_deeparg \
--arg_skip_fargene \
--run_bgc_screening false \
--save_db \
--outdir save-DBs

nextflow run nf-core/funcscan -r 2.0.0 \
-profile docker,test \
--run_amp_screening false \
--run_arg_screening \
--arg_skip_abricate \
--arg_skip_amrfinderplus \
--arg_skip_deeparg \
--arg_skip_fargene \
--arg_rgi_db ~/test-funcscan-error/save-DBs/databases/rgi/card_database_processed \
--run_bgc_screening false \
--save_db \
--outdir output-funcscan

[jasmezz]

Ok this behaviour is due to the fact that the CARD preprocessing module rgi/cardannotation is executed even if you provide an already preprocessed database. With the --save_db option, funcscan provides you both, preprocessed and non-preprocessed database folder. You can just use the non-processed one.

Usually, the double-preprocessing does not result in an error, that's why we decided to process the database always to be on the safe site. But with the pipeline-chaining, identical folder names would lead to overwriting, therefore causing the error. Thanks for reporting!

I'll create a fix to not execute the preprocessing module if the CARD database folder is recycled from a previous pipeline run.

[jasmezz]

Solved by #437