Bug in decoy creation

[ypriverol]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/pgdb pipeline documentation

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:
2. See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

Container engine

• Engine:
• version:
• Image tag:

Additional context

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/bin/pypgatk_cli.py", line 48, in <module>
      main()
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/bin/pypgatk_cli.py", line 44, in main
      cli()
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/click/core.py", line 829, in __call__
      return self.main(*args, **kwargs)
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/click/core.py", line 782, in main
      rv = self.invoke(ctx)
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/click/core.py", line 1259, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
      return ctx.invoke(self.callback, **ctx.params)
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/click/core.py", line 610, in invoke
      return callback(*args, **kwargs)
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/click/decorators.py", line 21, in new_func
      return f(get_current_context(), *args, **kwargs)
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/pypgatk/commands/proteindb_decoy.py", line 80, in generate_database
      proteindb_decoy.decoy_database()
    File "/opt/conda/envs/nf-core-pgdb-1.0dev/lib/python3.9/site-packages/pypgatk/proteomics/db/decoy_pyrat.py", line 233, in decoy_database
      fasta.close()
  AttributeError: 'FastaIterator' object has no attribute 'close'

Work dir:
  /Users/yperez/IdeaProjects/github-repo/BDP/nf-core-pgdb/work/19/d6ff3d5c551ee89fc0711ccf562903

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Failed to invoke `workflow.onComplete` event handler

 -- Check script 'main.nf' at line: 759 or see '.nextflow.log' file for more details

[ypriverol]

decoy tests has passed https://github.com/nf-core/pgdb/runs/1853421511?check_suite_focus=true