Standardize conversion workflow #1032
GitHub Actions / JUnit Test Report
failed
Sep 16, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
Annotations
github-actions / JUnit Test Report
nf.test-dataset_alevin_aligner
Assertion failed:
10 of 11 assertions failed
Raw output
Nextflow stdout:
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:ANNDATAR_CONVERT (Sample_X)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:ANNDATAR_CONVERT (Sample_X)` 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_X"
# load libraries
library(anndataR)
# read input
adata <- read_h5ad("Sample_X_alevin_results")
# convert to Rds
obj <- adata$to_Seurat()
# save files
saveRDS(obj, file = "Sample_X_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/6264e47732939bd9691cd8ea56b9ed1f/work/1b/d758497b6c1288e032ef5ef39c1998
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/6264e47732939bd9691cd8ea56b9ed1f/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/6264e47732939bd9691cd8ea56b9ed1f/meta/nextflow.log' file for details
Nextflow stderr:
Loading