Initialize new MitoPilot Project with user-provided mitogenome assemblies

Usage

new_project_userAsmb(
  path = ".",
  mapping_fn = NULL,
  mapping_id = "ID",
  data_path = NULL,
  assembly_path = "NA",
  genetic_code = 2,
  executor = c("local", "awsbatch", "NMNH_Hydra", "NOAA_SEDNA"),
  container = paste0("macguigand/mitopilot:", utils::packageVersion("MitoPilot")),
  config = 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, an `Assembly` column containing names of mitogenome assembly fasta files (one contig/scaffold sequence per sample), and a `Topology` column containing information about the assembly topology ("circular" or "linear") 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.
assembly_path: Path to the directory where the mitogenome assemblies are located. Can be a AWS s3 bucket even if not using AWS for pipeline execution.
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. Must be one of "local" (default) or "awsbatch", "NMNH_Hydra", or "NOAA_SEDNA".
container: The docker container to use for pipeline execution.
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.
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()`