Read names in a column on WGS table

[hkaspersen]

Is it possible to list the read names in a column on the WGS tab? This would be very helpful for us as we extract files from the tarballs.
Otherwise we have to grep the filename and do filtering for the read files themselves.

[magnulei]

So you want a column with fastq file names?
Lets see if it can be done.

This seems to be the format for the fastq files:
{Run Date}_{Machine ID}_{Sample Name}_S{x}_R{Read Number}_001_fastq.gz

In the above format, is "x" the sample number? Or something else? And how is it defined?
And the "001" at the end seems to never change? What does it mean?

Run Date, Machine ID and Sample Name are all available from the LIMS. And Read Number is always "1" and "2", so that part is also fine. Only unsure how to solve that S-number.

By the way, it would be so much neater to get both fastq file names and the tar-filenames directly from the source (ie the demultiplexing script) rather than reverse engineer it from the lims-side. Maybe something to think about when we get a connection between AWS and VI, @georgemarselis-nvi ?

[magnulei]

Putting this on hold for the time being.
If we in the future can hook up the shiny clarity app to the demultiplexing script we should implement this as a feature.

And I think Håkon was able to set up the ATLAS scripts without having the full fastq names.