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Add missing checkIfExists optoins (and language-server-formatting) #88

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GitHub Actions / JUnit Test Report failed Jan 28, 2025 in 0s. View latest attempt.

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

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Check failure on line 1 in Test pipeline: NFCORE_FUNCSCAN

github-actions / JUnit Test Report

Test pipeline: NFCORE_FUNCSCAN.test_taxonomy_prokka

Assertion failed: 

16 of 17 assertions failed

Raw output


            Nextflow stdout:

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

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_DATABASE_DOWNLOAD` terminated with an error exit status (126)


Command executed:

  ampcombi_download.py \
      --database_id DRAMP \
      --threads 1
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_DATABASE_DOWNLOAD":
      ampcombi: $(ampcombi --version | sed 's/ampcombi //')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/ampcombi:2.0.1--pyhdfd78af_0' locally
  2.0.1--pyhdfd78af_0: Pulling from biocontainers/ampcombi
  0cacab098358: Pulling fs layer
  bd9ddc54bea9: Pulling fs layer
  4e95c571d48f: Pulling fs layer
  0cacab098358: Verifying Checksum
  0cacab098358: Download complete
  0cacab098358: Pull complete
  bd9ddc54bea9: Verifying Checksum
  bd9ddc54bea9: Download complete
  bd9ddc54bea9: Pull complete
  4e95c571d48f: Verifying Checksum
  4e95c571d48f: Download complete
  4e95c571d48f: Pull complete
  Digest: sha256:3f790ebb57c8f4a1e8452f56a7405902be85c16134bff47add25dd42102b057e
  Status: Downloaded newer image for quay.io/biocontainers/ampcombi:2.0.1--pyhdfd78af_0
  /bin/bash: line 11: .command.run: Permission denied

Work dir:
  /home/runner/work/funcscan/funcscan/.nf-test/tests/c695303b4920bdf3902ed74a6265a3c/work/bc/8be4c4abef51940c1dbb8ee750cb15

Container:
  quay.io/biocontainers/ampcombi:2.0.1--pyhdfd78af_0

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '/home/runner/work/funcscan/funcscan/.nf-test/tests/c695303b4920bdf3902ed74a6265a3c/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/c695303b4920bdf3902ed74a6265a3c/meta/nextflow.log' file for details
Nextflow stderr:

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