Resources

When you run or export with the DockerTarget, resources are automatically added to the running container and stored under /resources. In case of the NativeTarget, this is not the case and since NextFlowTarget uses the NativeTarget it’s the same there. That does not mean that resources specified in functionality.yaml are not available in these cases, we only have to point to them where appropriate.

The following snippet (from ct/singler) illustrates this:

par = list(
  input = "input.h5ad",
  output = "output.h5ad",
  reference = "HPCA",
  outputField = "cellType",
  pruningMADS = 3,
  outputFieldPruned = "celltype-pruned",
  reportOutputPath = "report.md"
)
par$resources_dir <- resources_dir

In other words, resources_dir is automatically created by viash in all current 3 environments. This means that we can point to the report.Rmd file present in the resources like so:

rmarkdown::render(paste0(par$resources_dir, "/", "report.Rmd"), output_file = par$reportOutputPath)