Include cellrangerarc in checker #337
Merged
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
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:
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