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)
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