Initialize new MitoPilot Project

Usage

new_project(
  path = ".",
  mapping_fn = NULL,
  mapping_id = "ID",
  data_path = NULL,
  min_depth = 2e+06,
  genetic_code = 2,
  executor = c("local", "awsbatch", "slurm", "sge", "pbs", "lsf", "NMNH_Hydra",
    "NOAA_SEDNA"),
  container = paste0("macguigand/mitopilot:", utils::packageVersion("MitoPilot")),
  custom_seeds_db = NULL,
  custom_labels_db = NULL,
  config = NULL,
  profile_dir = mitopilot_config_dir(),
  ncbi_api_key = NULL,
  Rproj = TRUE,
  force = FALSE,
  ...
)

Arguments

path: Path to the project directory (default = current working directory)
mapping_fn: Path to a mapping file. Should be a csv that minimally includes an `ID` column with a unique identifier for each sample, a `Taxon` column containing taxonomic information for each sample, and columns `R1` and `R2` specifying the names of the raw paired read inputs. May include additional columns with other sample metadata.
mapping_id: The name of the column in the mapping file that contains the unique sample identifiers (default = "ID").
data_path: Path to the directory where the raw data is located. Can be a AWS s3 bucket even if not using AWS for pipeline execution..
min_depth: Minimum number of paired sequences after pre-processing to proceed with assembly (default: 2000000 reads)
genetic_code: Translation table for your organisms. See NCBI website for more info https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
executor: The executor to use for running the nextflow pipeline. May be a built-in template ("local" (default), "awsbatch", "slurm", "sge", "pbs", "lsf", "NMNH_Hydra", "NOAA_SEDNA") or the name of a saved cluster profile created with [generate_config()]. See [list_configs()] for available names.
container: The docker container to use for pipeline execution.
custom_seeds_db: Full path to custom seeds database for GetOrganelle
custom_labels_db: Full path to custom labels database for GetOrganelle
config: (optional) provide a path to an existing custom nextflow config file. If not provided a config file template will be created based on the specified executor.
profile_dir: Directory searched for saved cluster profiles when resolving `executor` (default [mitopilot_config_dir()]).
ncbi_api_key: Optional NCBI API key string. Used to raise NCBI request rate limits for the remote BLAST + GenBank fetch steps. See <https://www.ncbi.nlm.nih.gov/datasets/docs/v2/api/api-keys/>. May be left empty and edited later in `.config` (`params.ncbi_api_key`).
Rproj: (logical) Initialize and open an RStudio project in the project directory (default = TRUE). This option 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 as default processing parameters to `new_db()`