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Initialize a new RiboPilot project

Source: R/init_project.R
new_project.Rd

Mirrors MitoPilot's new_project(). Creates the project directory, copies the mapping file, initializes the SQLite tracking database, and writes a .config Nextflow config from the chosen executor template.

Usage

new_project(
  path = ".",
  mapping_fn = NULL,
  mapping_id = "ID",
  data_path = NULL,
  assembly_path = NULL,
  min_depth = 2e+06,
  executor = c("docker", "conda", "local", "slurm", "pbs", "sge", "lsf", "NMNH_Hydra",
    "NOAA_SEDNA"),
  container = paste0("macguigand/ribopilot:", utils::packageVersion("RiboPilot")),
  custom_seeds_db = NULL,
  custom_labels_db = NULL,
  ref_dir = NULL,
  config = NULL,
  profile_dir = ribopilot_config_dir(),
  ncbi_api_key = NULL,
  check_reads = TRUE,
  check_assemblies = TRUE,
  mapping_geome = "GEOME_BCID",
  fetch_geome = TRUE,
  mapping_gbif = "GBIF_ID",
  fetch_gbif = TRUE,
  mapping_ncbi = "BioSample",
  fetch_ncbi = TRUE,
  link_sources = FALSE,
  Rproj = TRUE,
  force = FALSE,
  ...
)

Arguments

path

Path to the project directory (default = current working dir).

mapping_fn

Path to a comma-separated mapping file. Minimally an ID column (unique sample id), a Taxon column, and R1/R2 columns naming the paired read files relative to data_path (or an Assembly column). Column names are matched ignoring case. Extra metadata columns are preserved.

mapping_id

Column in the mapping file with unique ids (default "ID").

data_path

Directory where the raw read data is located. Required when any sample lists reads; not needed when every sample supplies its own assembly.

assembly_path

Directory holding the assembly files named in the mapping file's optional Assembly column. A sample with an assembly is searched for its nuclear rDNA contigs instead of being assembled from reads, and its R1/R2 may be left blank. See dev/design/20_USER_ASSEMBLIES.md.

min_depth

Minimum number of reads left after trimming, counting both reads of a pair (2000000 is 1000000 pairs). A sample below it is not assembled and is marked Failed with a note.

executor

Executor for the Nextflow pipeline. Ready to use as-is: "docker" (default) and "local" run the RiboPilot container on this machine, and "NMNH_Hydra" and "NOAA_SEDNA" are ready-made Singularity profiles for those clusters. "conda" uses a self-installed conda env (not supported; warns). For any other cluster, build a profile with generate_config() and pass its name here. A bare scheduler name ("slurm", "sge", "pbs", "lsf") is an error: it has no queue or cluster options yet.

container

Container to use for pipeline execution.

custom_seeds_db

Path/URL to a custom GetOrganelle nr seeds database.

custom_labels_db

Path/URL to a custom GetOrganelle nr labels database.

ref_dir

Folder for built reference databases (default: the RIBOPILOT_REF_DIR environment variable, else ribopilot_ref_dir()).

config

Optional path to an existing custom Nextflow config file.

profile_dir

Directory searched for saved cluster profiles.

ncbi_api_key

Optional NCBI API key (raises request rate limits).

check_reads

(logical) Check that the read files named in the mapping file exist under data_path (default TRUE). Set FALSE when the data will be staged later.

check_assemblies

(logical) Check that the assembly files named in the mapping file exist under assembly_path (default TRUE).

mapping_geome

Name of the mapping-file column holding GEOME BCIDs (optional). Stored as GEOME_BCID. See vignette("Sample-Metadata"). Passed to new_db().

fetch_geome

Fetch GEOME metadata for samples with a BCID during setup (default TRUE). Set FALSE when offline and run fetch_geome() later. Passed to new_db().

mapping_gbif

Name of the mapping-file column holding GBIF occurrence IDs (optional). Stored as GBIF_ID. See vignette("Sample-Metadata"). Passed to new_db().

fetch_gbif

Fetch GBIF metadata for samples with a GBIF ID during setup (default TRUE). Set FALSE when offline and run fetch_gbif() later. Passed to new_db().

mapping_ncbi

Name of the mapping-file column holding NCBI BioSample or SRA accessions (optional). Must not be the sample ID column. Stored as BioSample. See vignette("Sample-Metadata"). Passed to new_db().

fetch_ncbi

Fetch NCBI metadata for samples with a BioSample value during setup (default TRUE). Set FALSE when offline and run fetch_ncbi() later. Passed to new_db().

Follow links between GEOME, GBIF, and NCBI records to fill in IDs a sample does not have yet (default FALSE). Saved as the project setting. See vignette("Sample-Metadata"). Passed to new_db().

Rproj

(logical) Initialize/open an RStudio project (default TRUE; no effect outside RStudio).

force

(logical) Recreate an existing project database (default FALSE). Without it, new_project() stops when the folder already holds a project.

...

Additional default processing parameters passed to new_db().