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Download sharded NCBI genome inputs into Bascet files

Source: R/ncbi_genomes.R
BascetDownloadNcbiGenomes.Rd

Runs bascet ncbi-genome-download once per .ncbilist shard produced by BascetPrepareNcbiGenomeFetchLists().

Usage

BascetDownloadNcbiGenomes(
  bascetRoot,
  inputName = "tofetch",
  outputName = "contigs",
  outFormat = "zip",
  threads = NULL,
  downloadStartsPerSecond = 2,
  queueSize = NULL,
  maxRetries = 5,
  keepTemp = FALSE,
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored.

inputName

Name of input .ncbilist shard prefix.

outputName

Name of output shard prefix.

outFormat

Output shard extension. Use "zip" to store {assembly}/contigs.fa entries, or "tirp.gz" to store contigs as R1 reads with dummy F quality scores and empty R2/UMI.

threads

Parallel genome workers per Bascet job. Defaults to runner ncpu.

downloadStartsPerSecond

Global per-job NCBI download start rate.

queueSize

Optional completed-fragment queue size.

maxRetries

Download retry count.

keepTemp

Keep per-job temporary download and fragment files.

overwrite

Whether to submit jobs when output files already exist.

runner

Bascet runner.

bascetInstance

Bascet instance.

Value

A zorn job object.