Fix test run (Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD')

[pawelciurkaardigen]

Description of the bug

Pipeline fails the tests (reporoduced locally)

Command used and terminal output

`nextflow run nf-core/funcscan -r 2.0.0 -profile test,docker --outdir test`


ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD` terminated with an error exit status (1)


Command executed:

  mkdir amp_ref_database/
  ampcombi_download.py
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD":
      ampcombi: $(ampcombi --version | sed 's/ampcombi //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/ampcombi:0.2.2--pyhdfd78af_0' locally
  0.2.2--pyhdfd78af_0: Pulling from biocontainers/ampcombi
  ca7680d1025d: Already exists
  bd9ddc54bea9: Already exists
  32ac20ce48fd: Pulling fs layer
  32ac20ce48fd: Verifying Checksum
  32ac20ce48fd: Download complete
  32ac20ce48fd: Pull complete
  Digest: sha256:e146a1e61af09d923f2dc7bd63ea8fa43b1c1aca18e139edeaf0f2da0720647f
  Status: Downloaded newer image for quay.io/biocontainers/ampcombi:0.2.2--pyhdfd78af_0
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  Traceback (most recent call last):
    File "/home/pawel_ciurka/.nextflow/assets/nf-core/funcscan/bin/ampcombi_download.py", line 78, in <module>
      download_DRAMP("amp_ref_database")
    File "/home/pawel_ciurka/.nextflow/assets/nf-core/funcscan/bin/ampcombi_download.py", line 49, in download_DRAMP
      for record in seq_record:
    File "/usr/local/lib/python3.11/site-packages/Bio/SeqIO/Interfaces.py", line 72, in __next__
      return next(self.records)
             ^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/Bio/SeqIO/FastaIO.py", line 246, in iterate
      Seq(sequence), id=first_word, name=first_word, description=title
      ^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/Bio/Seq.py", line 2034, in __init__
      self._data = bytes(data, encoding="ASCII")
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  UnicodeEncodeError: 'ascii' codec can't encode character '\u03a6' in position 1: ordinal not in range(128)

Relevant files

No response

System information

Nextflow version: 24.10.5

[pawelciurkaardigen]

Validating if fixed in 2.1.0

[pawelciurkaardigen]

In 2.1.0 DRAMP_DOWNLOAD was renamed to AMP_DATABASE_DOWNLOAD
Running nextflow run nf-core/funcscan -r 2.1.0 -profile test,docker --outdir test does not raise an error in AMP_DATABASE_DOWNLOAD module and it runs to completion