Initialize new MitoPilot Project with user-provided mitogenome assemblies

Usage

new_project_userAsmb(
  path = ".",
  mapping_fn = NULL,
  mapping_id = "ID",
  data_path = NULL,
  no_raw_data = FALSE,
  assembly_path = "NA",
  genetic_code = NULL,
  find_mitogenome = FALSE,
  mitofinder_db = NULL,
  attempt_circularization = FALSE,
  join_scaffolds = FALSE,
  executor = c("local", "awsbatch", "slurm", "sge", "pbs", "lsf", "NMNH_Hydra",
    "NOAA_SEDNA"),
  container = paste0("macguigand/mitopilot:", utils::packageVersion("MitoPilot")),
  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, and an `Assembly` column containing names of assembly fasta files. An optional `Topology` column ("circular" or "linear") declares the topology of a single-contig assembly; an assembly holding more than one contig is recorded as "multi" and any declaration is ignored. 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. Not required when `no_raw_data = TRUE`.
no_raw_data: (logical) Run without raw sequence data (default = FALSE). When TRUE, the read-mapping coverage step is skipped: `data_path` is ignored, coverage/depth statistics are left empty, and annotation coverage trimming is disabled. Use this to annotate an assembly you already have.
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: Optional NCBI translation table override. Default `NULL` auto-selects from each sample's curation ruleset; a number sets a project-wide override. https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
find_mitogenome: (logical) Search each supplied assembly for its mitochondrial contigs before the rest of the Assemble module runs (default = FALSE). Use this when your FASTA files hold whole assemblies rather than a mitogenome: contigs are BLASTed against the bundled metazoan mitogenome database, the survivors confirmed with MitoFinder, and only those carried forward. See [find_mito()].
mitofinder_db: Path to a MitoFinder GenBank database, built with [custom_assembly_db()] (`db_type = "mitofinder"`). Required when `find_mitogenome = TRUE`.
attempt_circularization: (logical) Attempt to circularize user assemblies during the Assemble module (default = FALSE). Every assembly is tried except a single-contig one already declared circular, and each contig is attempted on its own, so a fragmented assembly is eligible. Redundant overlap between a contig's ends is trimmed, and when raw reads are available the new junction must be supported by reads before that contig is called circular. Assemblies holding more than 100 contigs are left alone. Settings are editable later in the app's circularization options modal. See [circularize_asmb()].
join_scaffolds: (logical) Order a fragmented assembly against its BLAST reference into one joined sequence during the Assemble module (default = FALSE). Samples whose contigs match different reference mitogenomes are left alone. So is a sample with a junction the reference cannot size, since NCBI expects the number of Ns to be the estimated gap length. Because eligibility here is any multi-contig assembly rather than just mitogenome scaffolds, use this alongside `find_mitogenome = TRUE` so the join sees only confirmed mitochondrial contigs.
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.
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_userAsmb()]. Assembly parameters accepted by [new_db()] do not apply to a user-assembly project.