Initialize a test project for user-supplied assemblies — new_test_project

Sets up a test project for the user-assembly workflow, with nine samples that between them cover the shapes an assembly can arrive in: a linear mitogenome, a circular one, one that is circular but reported as linear, and six multi-contig assemblies: one holding a single mitogenome, one holding none, one holding two from different species, one holding a mitogenome that needs circularizing, one holding two mitogenomes of which one needs circularizing, and one holding a mitogenome split across three contigs. The assemblies ship with the package; the raw reads are the same fish data used by [new_test_project()].

Usage

new_test_project_userAsmb(
  path = ".",
  n = Inf,
  full_size = FALSE,
  executor = "local",
  container = paste0("macguigand/mitopilot:", utils::packageVersion("MitoPilot")),
  Rproj = TRUE,
  force = FALSE,
  ...
)

Arguments

path: path to the directory for the test project (default = current working directory). Will be created if it does not already exist.
n: how many samples to include in the test project (Default = Inf, include all)
full_size: (logical) Use the full size raw reads (default = FALSE). Setting to TRUE will download the reads from ENA, which will require several GB and will take some time to complete. By default the smaller pre-filtered read files packaged with MitoPilot are used.
executor: The executor to use for running the nextflow pipeline. A built-in template ("local" (default), "awsbatch", "slurm", "sge", "pbs", "lsf", "NMNH_Hydra", "NOAA_SEDNA") or a saved profile from [generate_config()]. See [list_configs()].
container: The container to use for running the pipeline.
Rproj: (logical) Initialize and open an RStudio project in the project directory (default = TRUE). This has no effect if not running interactively in RStudio.
force: (logical) Force recreating of existing project database and config files (default = FALSE).
...: Additional arguments passed to [new_project_userAsmb()]

Details

The project is created with the mitogenome search, the circularization attempt, and scaffold joining all switched on, since that is what these samples are for.