Hi All,

I am wondering what is the most widely used method/program/tool to automate the launch of bcl2fastq program as soon as the run finishes off on the Illumina machine. I am about to start writing my own custom shell script for the same; but before I do that I want to know whether ready-made solutions are already available.



The run folder nomenclature is as follows:

<a href="https://ibb.co/Lz5Jyj9"><img src="https://i.ibb.co/KjwLg4V/bcl.png" alt="bcl" border="0"></a>

**My idea would be like this -**

    Keep looking for folder containing the "Instrument Serial No." in its name:
            for every 15 minutes :
                Look inside the run log file for something which says - sequencing complete
                if YES:
                       Launch bcl2fastq
                else PASS:

If someone has better idea which could be implemented, please do let me know.

Hi 

Coming back to my own question with an answer. After a lot of careful considerations and talking to the Illumina people, it turned out that generation of `CopyComplete.txt` (NovaSeq) is a good trigger to start bcl2fastq. Here is a little bit more information on that:

1. `SequenceComplete.txt` indicates that the sequencing run has finished.
2. `CopyComplete.txt` is created by the Universal Copy Service (UCS) when all files have been copied to their destinations and run completion signal has been triggered.
3. `The RTAComplete.txt` file indicates that the images that are generated by the system have been converted to Basecalls. The Basecalls are stored as .bcl files. These bcl files can then be used as input for BCL2Fastq to produce the fastq files. 