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Add logic to skip cardannotation #55

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Add logic to skip cardannotation

Add logic to skip cardannotation #55

GitHub Actions / JUnit Test Report failed Jan 15, 2025 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

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Check failure on line 1 in Test pipeline: NFCORE_FUNCSCAN

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline: NFCORE_FUNCSCAN.test_preannotated_profile 

Assertion failed: 

17 of 28 assertions failed
Raw output 
Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN (sample_2)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN (sample_2)` terminated with an error exit status (1)


Command executed:

  DB_VERSION=$(ls card_database/card_database_*_all.fasta | sed "s/card_database\/card_database_v\([0-9].*[0-9]\).*/\1/")
  
  rgi \
      load \
       \
      --card_json card_database/card.json \
      --debug --local \
      --card_annotation card_database/card_database_v$DB_VERSION.fasta \
      --card_annotation_all_models card_database/card_database_v$DB_VERSION\_all.fasta \
  
  
  rgi \
      main \
      --alignment_tool BLAST --data NA    --split_prodigal_jobs \
      --num_threads 4 \
      --output_file sample_2 \
      --input_sequence wastewater_metagenome_contigs_2.fasta
  
  mkdir temp/
  for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e $FILE ]] && mv $FILE temp/; done
  
  RGI_VERSION=$(rgi main --version)
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN":
      rgi: $(echo $RGI_VERSION)
      rgi-database: $(echo $DB_VERSION)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/rgi:6.0.3--pyha8f3691_1' locally
  6.0.3--pyha8f3691_1: Pulling from biocontainers/rgi
  ca7680d1025d: Already exists
  bd9ddc54bea9: Already exists
  4a384d4223dd: Pulling fs layer
  4a384d4223dd: Verifying Checksum
  4a384d4223dd: Download complete
  4a384d4223dd: Pull complete
  Digest: sha256:2ef0a291697b721b6e7ca2a328f7b7c4f338a962468cf13885a3c734777c326b
  Status: Downloaded newer image for quay.io/biocontainers/rgi:6.0.3--pyha8f3691_1
  ls: card_database/card_database_*_all.fasta: No such file or directory

Work dir:
  /home/runner/work/funcscan/funcscan/.nf-test/tests/1f6a72c94a9e6a86afed0ba5b15fed82/work/19/bf3fa7b8010a1d3c287ba2b66f2aca

Container:
  quay.io/biocontainers/rgi:6.0.3--pyha8f3691_1

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/funcscan/funcscan/.nf-test/tests/1f6a72c94a9e6a86afed0ba5b15fed82/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/funcscan/funcscan/.nf-test/tests/1f6a72c94a9e6a86afed0ba5b15fed82/meta/nextflow.log' file for details
Nextflow stderr:
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