Adding cellrangermulti subworkflow #805
GitHub Actions / JUnit Test Report
failed
Feb 26, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
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Check failure on line 1 in test-dataset_alevin_aligner
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:
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