Add script to sort NextSeq runs

illumina/sort-nextseq.jl

@@ -0,0 +1,44 @@
+#!/usr/bin/julia
+# Renames the FASTQ files in a directory by prepending the sample number based
+# on the embedded sample number
+
+# Activate the proper packages
+using Tk
+
+# Prompt for the folder containing the FASTQs
+fastq_folder = ChooseDirectory()
+
+# Get all of the files
+fastqs = readdir(fastq_folder)
+
+# Iterate through each file
+for fastq in fastqs
+    # Get the full path
+    fastq_path = joinpath(fastq_folder, fastq)
+
+    # Delete if this is a JSON file
+    if last(fastq,5) == ".json"
+        rm(fastq_path)
+        println(string("Deleting ", fastq_path))
+        continue
+    end
+
+    # Find the sample number in the filename
+    startS = findfirst("_S", fastq)
+    startL = findfirst("_L", fastq)
+
+    # Extract the sample number
+    sampleId = fastq[(startS[1]+1):(startL[1]-1)]
+
+    # Convert the number to three digits, no matter what
+    sampleNum = parse(Int64, sampleId[2:end])
+    sampleId = string("S", lpad(sampleNum, 3, "0"))
+
+    # Construct the new filename
+    fastq_newname = string(sampleId, "_", fastq)
+
+    # Rename the file
+    mv(fastq_path, joinpath(fastq_folder, fastq_newname))
+    println(string("Renaming ", fastq_path, " to ", joinpath(fastq_folder, fastq_newname)))
+
+end