Create datasets from annotation file

saveRDS(snakemake, snakemake@log$snakemake)
source(snakemake@params$setup, echo=FALSE)

outFile       <- snakemake@output$colData
annoFile      <- snakemake@input$sampleAnnoFile
fileMapFile   <- snakemake@params$fileMapping

name <- snakemake@wildcards$dataset
anno    <- fread(annoFile)
mapping <- fread(fileMapFile)

subset_ids <- snakemake@params$ids
annoSub <- anno[RNA_ID %in% subset_ids]
setnames(annoSub, "RNA_ID", "sampleID")
colData <- merge(annoSub,
    mapping[FILE_TYPE == "RNA_BAM_FILE", .(sampleID=ID, bamFile=FILE_PATH)])
setcolorder(colData, unique(c("sampleID", "STRAND", "PAIRED_END", "bamFile"), colnames(annoSub)))

Dataset: all

Final sample table all

DT::datatable(finalTable, options=list(scrollX=TRUE))

dim(finalTable)

## [1] 100  20

write_tsv(finalTable, file=outFile)