Standardize conversion workflow #1042
GitHub Actions / JUnit Test Report
failed
Oct 4, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
Annotations
github-actions / JUnit Test Report
nf.test-dataset_cellranger_aligner
Assertion failed:
8 of 13 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_raw_matrix.h5ad")
# convert to Rds
obj <- adata$to_Seurat()
# save files
dir.create(file.path("Sample_X"), showWarnings = FALSE)
saveRDS(obj, file = "Sample_X/Sample_X_raw_matrix.Rds")
Command exit status:
125
Command output:
(empty)
Command error:
docker: invalid reference format.
See 'docker run --help'.
Work dir:
/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/17493f5b507e3df5263c89c8572a97f1/work/87/5777e27aa0a7e4e8466cb0838049b4
Container:
docker://fmalmeida/anndatar:dev
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/17493f5b507e3df5263c89c8572a97f1/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/17493f5b507e3df5263c89c8572a97f1/meta/nextflow.log' file for details
Nextflow stderr:
Loading