This function will set up a test project and fectch associated data from ENA. The `n` parameter can be used to limit the number of species used in the test project for faster set up.
Usage
new_test_project(
path = ".",
n = Inf,
full_size = FALSE,
executor = "local",
container = paste0("macguigand/mitopilot:", utils::packageVersion("MitoPilot")),
Rproj = TRUE,
force = FALSE,
fetch_metadata = TRUE,
...
)Arguments
- path
path the the directory for the test project (default = currect working directory). Will be created if it does not already exists.
- n
how many samples to include in the test project (Default = Inf, include all)
- full_size
(logical) Use the full size test data set (default = FALSE). Setting to TRUE will download the raw data from ENA, which will require 10GB and will take some time to complete. By default a set of smaller pre-filtered input files will be fetched from the MitoPilot github repo.
- 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 now effect if not running interactively in RStudio.
- force
(logical) Force recreating of existing project database and config files (default = FALSE).
- fetch_metadata
(logical) Fetch each sample's NCBI metadata (synthetic samples use their source run's) and follow links to GBIF and GEOME (default = TRUE). Linking is saved as the project setting. Set FALSE when offline.
- ...
Additional arguments passed `init_db()`