Fsharp cwl

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx

@@ -4,22 +4,22 @@
 
 #r "nuget: ARCtrl.NET"
 #r "nuget: ARCtrl.QueryModel"
+#r "nuget: FsSpreadsheet.CsvIO"
 
-open System.IO
 open ARCtrl.NET
 open ARCtrl
 open ARCtrl.QueryModel
 open ARCtrl.Helper
-open FsSpreadsheet
 open FsSpreadsheet.Net
+open FsSpreadsheet.CsvIO
 
 // input parameters
 
-// let args : string array = fsi.CommandLineArgs |> Array.tail
-// let arcPath = args.[0]
-// let assayName = args.[1]
-// let startingNodeNum = args.[2] |> int
-// let outName = args.[3]
+let args : string array = fsi.CommandLineArgs |> Array.tail
+let arcPath = args.[0]
+let assayName = args.[1]
+let startingNodeNum = args.[2] |> int
+let outName = args.[3]
 
 
 type ArcTables with
@@ -31,16 +31,16 @@ type ArcTables with
         )
         |> ArcTables
 
-// test parameters
-let source = __SOURCE_DIRECTORY__
-let arcPath = Path.Combine(source, "../../")
-let assayName = "Talinum_RNASeq_minimal"
-let startingNodeNum = 0
-let outName = "rnaseq-samples"
+// // test parameters
+// let source = __SOURCE_DIRECTORY__
+// let arcPath = Path.Combine(source, "../../")
+// let assayName = "Talinum_RNASeq_minimal"
+// let startingNodeNum = 0
+// let outName = "rnaseq-samples"
 
 // Load ARC
 
-// Remove all tables with either an input or output column missing 🤣😀
+// Remove all tables with either an input or output column missing
 let clean (a : ARC)  = 
     a.ISA.Value.Assays |> Seq.iter (fun a -> 
         a.Tables
@@ -64,7 +64,7 @@ let clean (a : ARC)  =
     )
     a
 
-// transform all data cells to freetext cells 😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀
+// transform all data cells to freetext cells
 let shittify (a : ARC) = 
     a.ISA.Value.Assays |> Seq.iter (fun a -> 
         a.Tables
@@ -161,6 +161,8 @@ let wb = new FsSpreadsheet.FsWorkbook()
 
 wb.AddWorksheet ws
 
-// Write to csv
+// Write to xlsx
+wb.ToXlsxFile ($"{outName}.xlsx")
 
-wb.ToXlsxFile (outName + ".xlsx")
\ No newline at end of file
+// Write to csv
+wb.ToCsvFile ($"{outName}.csv")
\ No newline at end of file