Standardize conversion workflow #1032
GitHub Actions / JUnit Test Report
failed
Sep 16, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
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github-actions / JUnit Test Report
nf.test-dataset_star_aligner
Assertion failed:
4 of 12 assertions failed
Raw output
Nextflow stdout:
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:ANNDATAR_CONVERT (Sample_Y)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:ANNDATAR_CONVERT (Sample_Y)` terminated with an error exit status (125)
Command executed [/home/runner/work/scrnaseq/scrnaseq/./workflows/../subworkflows/local/../../modules/local/templates/anndatar_convert.R]:
#!/usr/bin/env Rscript
# to use nf variables: "Sample_Y"
# load libraries
library(anndataR)
# read input
adata <- read_h5ad("Sample_Y_filtered_matrix.h5ad")
# convert to Rds
obj <- adata$to_Seurat()
# save files
saveRDS(obj, file = "Sample_Y_standardized.Rds")
Command exit status:
125
Command output:
(empty)
Command error:
Unable to find image 'quay.io/fmalmeida/anndatar:dev' locally
docker: Error response from daemon: unauthorized: access to the requested resource is not authorized.
See 'docker run --help'.
Work dir:
/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/250ef629f95a430ee19e521cdfb63f8c/work/a7/6cc94332fbb3a88ba047d7887c02b0
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/250ef629f95a430ee19e521cdfb63f8c/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/250ef629f95a430ee19e521cdfb63f8c/meta/nextflow.log' file for details
Nextflow stderr:
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