Prototype sabre - demultiplexing addition to RNAsik

[serine]

Hi world,

Putting this out there hoping that somebody can get involved and write this bit of code for me :) :+1: . This is great way to get involved with open-source, learn and practice not only code writing by PR (pull request) submission, code review and perhaps some git rebasing - so that this new feature comes as a single unit. Don't be afraid if you haven't done this below, just fork the repo and see if you can make this bit of code to work. I can help you with the rest.

Below I've tried to described as detailed as I could what's needs doing in a step by step manner.

• new flag -demult used to indicate that demultiplexing need to take place before running alignement
• fastq files are passed in through -fqDir
• error out if more then two fastq files were found and -demult is give. There probably can be just one fastq files (haven't seen that yet)
• barcodes need to be passed through samplesSheet. Have to be a bit smart about handling different cases i.e normal RNAseq vs demultiplex first runs, because in a normal RNAseq run the columns order and meaning is "old_prefix" "new_prefix", whereas for demultiplexing run it should be "sample_name", "barcode".
• if -demult flaged make new directory under fastqDir i.e fastqDir/demultiplexed similar to

sikFqFiles.bds:18:    string fqDir = sikDir+"/"+"fastqDir/"
sikTrim.bds:13:    string trimedDir = sikDir+"/"+"fastqDir/trimed"

• write a function getDemultFqFiles in a separate sikDemultiplex.bds file. This function runs sabre and returns a list of demutltiplexed fastq files. This is how I think it should be pluged into main running script.

diff --git a/src/RNAsik.bds b/src/RNAsik.bds
index 83beaaf..65924c8 100644
--- a/src/RNAsik.bds
+++ b/src/RNAsik.bds
@@ -62,7 +62,14 @@ string{} usrOpts = getUsrOpts(extraOpts)

 string[] fqFiles
 if(!fqDir.isEmpty()) {
-    fqFiles = getFqFiles(cmdExe, fqDir, extn, sikDir)
+
+    if(demult) {
+        fqFile = getDemultFqFiles(....)
+    }
+    else {
+        fqFiles = getFqFiles(cmdExe, fqDir, extn, sikDir)
+    }
+
     mkLog("fqFiles", parseList(fqFiles), "samples", logsDir)

     if(trim) {

in fact for cleaner code perhaps move if(trim) into if else(trim) block. As in try demultiplexing, then try trimming, then simply get fastq files from fqDir path

Also need to think about some test cases

cheers