run_salmon: Generate commands to run salmon

In IMBEIbioinformatics/BIUMmisc: A collection of functions and scripts commonly used by the BIUM-MZ Core Facility and the Bioinformatics group at the IMBEI

Generate commands to run salmon

Description

Generate commands to run salmon on the files from a standardized sample sheet as the ones we exchange with collaboration partners

Usage

run_salmon(
  samples_info_sheet,
  salmon_bin = "salmon",
  salmon_index_dir,
  salmon_output_dir = "_quants",
  quants_prefix = "sample_scenarioid_sampleid_",
  salmon_ncores = 12,
  salmon_options = "--validateMappings",
  create_script = TRUE,
  script_name = "salmonrunner.sh",
  display_commands = TRUE,
  force = FALSE
)

Arguments

samples_info_sheet	Character string,
salmon_bin	Character, specifying the name of the executable to be run as salmon. Defaults to "salmon", which is perfectly fine if the tool is available in the PATH, be that system wide or (even better) with a conda environment
salmon_index_dir	Character, defines the folder where the salmon index is located. Needs to be specified by the user.
salmon_output_dir	Character, specifies the folder where the outputs of salmon will be written into. Sensibly defaults to "_quants", which matches the folder structure we are familiar with
quants_prefix	Character - what string should be prepended to the values of the id field in the samples_info_sheet
salmon_ncores	Numeric, number of cores to be used by salmon
salmon_options	Character string, contains all additional salmon parameters. Defaults to --validateMappings, but could also be an empty string or set to NULL
create_script	Logical value, whether to create or not a script - its name is specified by script_name
script_name	Character string, name of the script to write commands into. Defaults to "salmonrunner.sh"
display_commands	Logical, whether to print out to the console the commands as message. Defaults to TRUE
force	Logical value, whether to overwrite the file in script_name if already existing. Defaults to FALSE

Value

Invisible NULL, the function prints out the commands as messages and as a file, optionally

Examples

mysheet <- samplesheet_creator(ss_filename = "mysheet", ss_dir = tempdir())
run_salmon(readxl::read_excel(mysheet), salmon_index_dir = "/myindex/dir",
           create_script = FALSE)

IMBEIbioinformatics/BIUMmisc documentation built on June 12, 2025, 10:50 p.m.