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Initialize a new RiboPilot project database

Source: R/init_db.R
new_db.Rd

Creates the SQLite tracking database. Mirrors MitoPilot's new_db() spine (samples / preprocess / pre_opts / assemble / assemble_opts / blast_opts / assemblies) but with nuclear ribosomal (nrDNA) assembly options. Annotation, curation, and export tables are added in later build increments.

Usage

new_db(
  db_path = "./.sqlite",
  mapping_fn = NULL,
  mapping_id = "ID",
  mapping_taxon = "Taxon",
  data_path = NULL,
  assembly_path = NULL,
  check_reads = TRUE,
  check_assemblies = TRUE,
  assemble_cpus = 6,
  assemble_memory = 24,
  seeds_db = NULL,
  labels_db = NULL,
  getOrganelle = paste("-F anonym", "-R 10 -k 21,45,65,85,105,115", "--larger-auto-ws"),
  max_paths = 10,
  max_scaffolds = 10,
  min_assembly_length = 500,
  ref_dir = NULL,
  mapping_geome = "GEOME_BCID",
  fetch_geome = TRUE,
  mapping_gbif = "GBIF_ID",
  fetch_gbif = TRUE,
  mapping_ncbi = "BioSample",
  fetch_ncbi = TRUE,
  link_sources = FALSE
)

Arguments

db_path

Path to the new database file.

mapping_fn

Path to the mapping CSV (columns ID, Taxon, R1, R2).

mapping_id

Column name to use as the primary key (default "ID").

mapping_taxon

Column name with a taxonomic identifier (default "Taxon").

data_path

Directory holding the raw read files named in the mapping file. Read files are resolved as <data_path>/<R1>, the same way the Nextflow pipeline does it. When NULL, read files cannot be located and only the paired-end check is applied.

assembly_path

Directory holding the assembly files named in the mapping file's optional Assembly column. A sample with an assembly skips read preprocessing and assembly: its nuclear rDNA contigs are found inside the supplied file instead. Its R1/R2 may be blank.

check_reads

(logical) Check that the read files named in the mapping file exist (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).

assemble_cpus

Default number of CPUs for assembly.

assemble_memory

Default memory (GB) for assembly.

seeds_db

Path or URL to the GetOrganelle seeds database. NULL (default) names an Actinopterygii database that RiboPilot does not ship; the Reference step replaces it.

labels_db

Path or URL to the GetOrganelle labels database. NULL (default) names an Actinopterygii database that RiboPilot does not ship; the Reference step replaces it.

getOrganelle

Default GetOrganelle command-line options.

max_paths

Max assembly paths for a sample to continue (default 10).

max_scaffolds

Max contigs within a path to continue (default 10).

min_assembly_length

Minimum contig length (bp) to retain (default 500).

ref_dir

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

mapping_geome

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

fetch_geome

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

mapping_gbif

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

fetch_gbif

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

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").

fetch_ncbi

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

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").