library(workflows)
checkpoint_file <- commandArgs(trailingOnly=TRUE)[1]
clobber <- as.logical(commandArgs(trailingOnly=TRUE)[2])
libraries <- commandArgs(trailingOnly=TRUE)[3:length(commandArgs(trailingOnly=TRUE))]
for ( lib in libraries ) library(lib, character.only=TRUE)
this_pipeline <- readRDS(checkpoint_file)
this_pipeline <- execute(this_pipeline, clobber=clobber)
checkpoint(this_pipeline)
this_success_filename <- file.path(this_pipeline$working_directory, '_sge-logs',
paste0(basename(this_pipeline$checkpoint_filename), '.success'))
writeLines(this_success_filename, this_success_filename)
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