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Standardize conversion workflow #1034

Standardize conversion workflow

Standardize conversion workflow #1034

GitHub Actions / JUnit Test Report failed Sep 26, 2024 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

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nf.test-dataset_kallisto_aligner

Assertion failed: 

7 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("counts_unfiltered")
  
  # convert to Rds
  obj <- adata$to_Seurat()
  
  # save files
  dir.create(file.path("Sample_Y"), showWarnings = FALSE)
  saveRDS(obj, file = "Sample_Y/Sample_Y_null_matrix.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/22ea1c4ecf262148ed1ee87e15c67438/work/9c/89e9617d07e3c2e443ce2bacd5f14b

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/22ea1c4ecf262148ed1ee87e15c67438/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/22ea1c4ecf262148ed1ee87e15c67438/meta/nextflow.log' file for details
Nextflow stderr: