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

[jasmezz]

Update from my side: I can reproduce the error and it occurs in these cases:

• if only 1 AMP tool is executed
• if multiple tools are executed but only 1 tool could identify any AMPs
• if multiple tools are executed but no tool could identify any AMPs

Example output if two tools are executed (ampir and macrel), both their output files are handed to ampcombi/parsetables correctly, but contain no AMP hits. The missing AMPs apparently cause the parsetables module to crash:

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.ampir.tsv' '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

It occurs not only on dev branch, but also on the current add_interproscan_to_amp branch which is supposed to fix it. So it probably has to be fixed upstream in AMPcombi, @Darcy220606?

[Darcy220606]

Thank you for detecting and reporting the problem @amizeranschi 💚

It seems the error is after all caused by the output declaration in the nf-core module for ampcombi2/parsetables.

AMPcombi itself handles samples with no AMPs predicted and reports that in the sample log file in the sample directory. The issue is as Jasmin and yourself reported Missing output file(s) sample_2/contig_gbks/expected by processNFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_2)`` because in the module it expects all output files in the output directory therefore the sample output directory files must all be optional.

Ive fixed that in nf-core/modules#7458. Once that PR is merged and the module updated in the pipeline this error should be fixed.

[Darcy220606]

This has been addressed and solved in #428