Skip to contents

Write sharded SRA accession lists for later import

Source: R/sra_import.R
BascetPrepareSraFetchLists.Rd

BascetPrepareSraFetchLists() reads an SRA RunInfo table, orders runs by cell name, and writes one .sralist file per zorn shard. These files are intended as inputs to external download jobs that later feed bascet import-sra.

Usage

BascetPrepareSraFetchLists(
  runinfo,
  bascetRoot,
  outputName = "tofetch",
  numShards = NULL,
  runsPerShard = 1000,
  runColumn = "Run",
  cellColumn = NULL,
  overwrite = FALSE
)

Arguments

runinfo

SRA RunInfo data frame, or path to a RunInfo CSV file.

bascetRoot

The root folder where all Bascets are stored.

outputName

Name of output shard prefix.

numShards

Number of .sralist files to create. If NULL, this is derived from runsPerShard.

runsPerShard

Target number of SRA runs per .sralist when numShards is NULL.

runColumn

Column containing SRA run accessions.

cellColumn

Column used for alphabetic cell ordering.

overwrite

Overwrite existing output files.

Value

A data frame describing run-to-shard assignment.