Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Include cellrangerarc in checker #337

Merged
merged 1 commit into from
Jun 4, 2024

Include cellrangerarc in checker

20a6b46
Select commit
Loading
Failed to load commit list.
Sign in for the full log view
Merged

Include cellrangerarc in checker #337

Include cellrangerarc in checker
20a6b46
Select commit
Loading
Failed to load commit list.
GitHub Actions / JUnit Test Report failed Jun 4, 2024 in 0s

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

Annotations

Check failure on line 1 in test-dataset_star_aligner

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test-dataset_star_aligner

Assertion failed: 

11 of 12 assertions failed
Raw output
Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (GRCm38.p6.genome.chr19.fa)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (GRCm38.p6.genome.chr19.fa)` terminated with an error exit status (125)

Command executed:

  filter_gtf_for_genes_in_genome.py \
      --gtf gencode.vM19.annotation.chr19.gtf \
      --fasta GRCm38.p6.genome.chr19.fa \
      -o GRCm38.p6.genome.chr19_genes.gtf
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/python:3.9--1' locally
  docker: Error response from daemon: Head "https://quay.io/v2/biocontainers/python/manifests/3.9--1": Get "https://quay.io/v2/auth?scope=repository%3Abiocontainers%2Fpython%3Apull&service=quay.io": net/http: request canceled (Client.Timeout exceeded while awaiting headers).
  See 'docker run --help'.

Work dir:
  /home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/40abbf174dec39ee94268011514d321a/work/7d/3889b3113bc7dd115b0f1b3d3b2def

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/scrnaseq/scrnaseq/.nf-test/tests/40abbf174dec39ee94268011514d321a/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/scrnaseq/scrnaseq/.nf-test/tests/40abbf174dec39ee94268011514d321a/meta/nextflow.log' file for details
Nextflow stderr: