AMP screening doesn't run when only a single tool is enabled

[amizeranschi]

Testing the latest dev version, the AMP subworkflow is failing when only one tool is enabled. The following command reproduces the error:

nextflow pull nf-core/funcscan -r dev

nextflow run nf-core/funcscan -r 640992df1213c6f7b48514aac65790ee3e59f0d2 \
-profile docker,test \
--run_amp_screening \
--amp_skip_ampir \
--amp_skip_amplify \
--amp_cutoff 0.4 \
--save_db \
--outdir test-funcscan

And this is the error:

ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_2)'

Caused by:
  Missing output file(s) `sample_2/contig_gbks/` expected by process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_2)`


Command executed:

  ampcombi parse_tables \
      --path_list 'sample_2.macrel.prediction' \
      --faa sample_2_pyrodigal.faa \
      --gbk sample_2_pyrodigal.gbk \
      --sample_list sample_2 \
      --amp_database DRAMP \
      --amp_database_dir amp_DRAMP_database \
       \
      --aminoacid_length 120 --db_evalue 5 --amp_cutoff 0.6 --ampir_file .ampir.tsv --amplify_file .amplify.tsv --macrel_file .macrel.prediction --hmmsearch_file .hmmer_hmmsearch.txt --ampgram_file '.tsv' --amptransformer_file '.txt' --neubi_file '.fasta' --log TRUE --hmm_evalue 0.06 --window_size_stop_codon 60 --window_size_transporter 11 \
      --threads 4
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES":
      ampcombi: $(ampcombi --version | sed 's/ampcombi //')
  END_VERSIONS

Command exit status:
  0

Command output:
  Success: 'ampcombi parse_tables' completed successfully ! Now run ampcombi complete !

Work dir:
  /home/ubuntu/work/13/797b8689104e7223dd481e32307d75

The following warning is also shown. This seems to be a separate issue, so I'll open a separate report for it.

WARN: The following invalid input values have been detected:

* --amp_cutoff: 0.4

[jasmezz]

Will be fixed in #428