Process batches using SLURM by selecting directories

Choose which batches to process by selecting the directory where the measurement files are stored. It will create the necessary files for submission of the job to the workflow manager SLURM in `saveDirectory`.

Usage

screeningSelectedBatchesSlurm(
  msrawfileIndex,
  batchDirs,
  saveDirectory,
  email,
  screeningType = "dbas"
)

Arguments

msrawfileIndex

Name of index where processing information is stored

batchDirs

Directory of measurement files (recursive, multiple permitted)

saveDirectory

Location where files will be saved. Directory will be created. Warning: files may be overwritten if the directory already exists

email

Email recipient for SLURM notifications

screeningType

either 'dbas' or 'nts' for library screening and non-target-screening, respectively

Details

Three files are created, the records of all files to process, organized into batches (.RDS); the R script which SLURM needs to run, and the SLURM job file (`.sbatch`). The command needed to start the process is given as a message (you may need to switch to a SLURM-enabled server).

Examples

if (FALSE) { # \dontrun{
userEmail <- "example@bafg.de"
dirResults <- "processingResults"
msrawfileIndexName <- "ntsp25.2_msrawfiles"
library(ntsportal)
connectNtsportal()
file.remove(list.files(dirResults, f = T))

screeningSelectedBatchesSlurm(
  msrawfileIndex = msrawfileIndexName,
  batchDirs = "/root/dir/all/msrawfiles",
  saveDirectory = dirResults,
  email = userEmail
)
} # }