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Adding cellrangermulti subworkflow #805

Adding cellrangermulti subworkflow

Adding cellrangermulti subworkflow #805

GitHub Actions / JUnit Test Report failed Feb 26, 2024 in 0s

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

Annotations

Check failure on line 1 in test-dataset_alevin_aligner

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@github-actions github-actions / JUnit Test Report

test-dataset_alevin_aligner

Assertion failed: 

10 of 11 assertions failed
Raw output
Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GRCm38.p6.genome.chr19_genes.gtf)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GRCm38.p6.genome.chr19_genes.gtf)` terminated with an error exit status (125)

Command executed:

  # export required var
  export ALEVIN_FRY_HOME=.
  export NUMBA_CACHE_DIR=.
  
  # prep simpleaf
  simpleaf set-paths
  
  # run simpleaf index
  simpleaf \
      index \
      --threads 2 \
      --fasta GRCm38.p6.genome.chr19.fa \
      --gtf GRCm38.p6.genome.chr19_genes.gtf \
      --rlen 91 \
      -o salmon
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX":
      simpleaf: $(simpleaf -V | tr -d '\n' | cut -d ' ' -f 2)
      salmon: $(salmon --version | sed -e "s/salmon //g")
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/simpleaf:0.10.0--h9f5acd7_1' locally
  docker: Error response from daemon: Get "https://quay.io/v2/": net/http: request canceled (Client.Timeout exceeded while awaiting headers).
  See 'docker run --help'.

Work dir:
  /home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/dda1af5df5c0a5116e338282da85a271/work/8c/97e077238510e0d21256009357f5c1

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/scrnaseq/scrnaseq/.nf-test/tests/dda1af5df5c0a5116e338282da85a271/meta/nextflow.log' file for details
Nextflow stderr: