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Standardize conversion workflow #1032

Standardize conversion workflow

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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Check failure on line 1 in nf

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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/27/9deba61a22fcae6435d393e1d5fc14

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/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: