Download sharded SRA run lists into Bascet TIRP files

Runs bascet import-sra once per .sralist shard. The Bascet command calls SRA Toolkit and writes indexed TIRP output directly.

Usage

BascetDownloadSraRuns(
  bascetRoot,
  inputName = "tofetch",
  outputName = "filtered",
  runinfo = NULL,
  threads = NULL,
  runsAhead = 10,
  sraWorkers = NULL,
  overwrite = FALSE,
  keepTemp = FALSE,
  prefetch = "prefetch",
  fasterqDump = "fasterq-dump",
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored.

inputName

Name of input .sralist shard prefix.

outputName

Name of output TIRP shard prefix.

runinfo

Optional RunInfo CSV. Defaults to <inputName>.runinfo.csv if present in bascetRoot.

threads

Threads passed to fasterq-dump. Defaults to runner ncpu.

runsAhead

Maximum number of completed fasterq-dump outputs buffered ahead of TIRP writing.

sraWorkers

Number of concurrent SRA Toolkit workers. If NULL, Bascet uses threads.

overwrite

Whether to submit jobs when output files already exist.

keepTemp

Keep per-run SRA/FASTQ scratch files.

prefetch

Path to SRA Toolkit prefetch executable.

fasterqDump

Path to SRA Toolkit fasterq-dump executable.

runner

Bascet runner.

bascetInstance

Bascet instance.

Value

A zorn job object.