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Merge pull request #793 from d4straub/update-modules-2.12.0dev #1603

Merge pull request #793 from d4straub/update-modules-2.12.0dev

Merge pull request #793 from d4straub/update-modules-2.12.0dev #1603

GitHub Actions / JUnit Test Report failed Nov 13, 2024 in 0s

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

Annotations

Check failure on line 1 in Custom DADA2 Reference Taxonomy Database

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Custom DADA2 Reference Taxonomy Database

Assertion failed: 

23 of 25 assertions failed
Raw output
Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:UNTAR (85_greengenes.tar.gz)'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:UNTAR (85_greengenes.tar.gz)` terminated with an error exit status (2)


Command executed:

  mkdir user
  
  ## Ensures --strip-components only applied when top level of tar contents is a directory
  ## If just files or multiple directories, place all in prefix
  if [[ $(tar -taf 85_greengenes.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C user --strip-components 1 \
          -xavf \
           \
          85_greengenes.tar.gz \
  
  else
      tar \
          -C user \
          -xavf \
           \
          85_greengenes.tar.gz \
  
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:UNTAR":
      untar: $(echo $(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  2

Command output:
  85_greengenes.tax
  85_greengenes.fna

Command error:
  Unable to find image 'quay.io/nf-core/ubuntu:20.04' locally
  20.04: Pulling from nf-core/ubuntu
  99803d4b97f3: Pulling fs layer
  99803d4b97f3: Verifying Checksum
  99803d4b97f3: Download complete
  99803d4b97f3: Pull complete
  Digest: sha256:59e9d08d8dc153bfc704de15af5b14ac82f5ac695377fa29dd5087b6fea7942e
  Status: Downloaded newer image for quay.io/nf-core/ubuntu:20.04
  
  gzip: stdin: unexpected end of file
  tar: Unexpected EOF in archive
  tar: Error is not recoverable: exiting now
  85_greengenes.tax
  85_greengenes.fna
  
  gzip: stdin: unexpected end of file
  tar: Unexpected EOF in archive
  tar: Unexpected EOF in archive
  tar: Error is not recoverable: exiting now

Work dir:
  /home/runner/work/ampliseq/ampliseq/.nf-test/tests/ee01a448636d56e7fe65cc46a67aa9a6/work/39/1564899eba7179067d4f1f69b0bdf5

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '/home/runner/work/ampliseq/ampliseq/.nf-test/tests/ee01a448636d56e7fe65cc46a67aa9a6/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/ampliseq/ampliseq/.nf-test/tests/ee01a448636d56e7fe65cc46a67aa9a6/meta/nextflow.log' file for details
Nextflow stderr:

Nextflow 24.10.0 is available - Please consider updating your version to it