As a prod bioinfo member I want the iSeq runs to be demultiplexed automatically so that I don't have to spend time on manually starting the demultiplexing.
Problem:
There is no procedure for demultiplexing of iSeq runs set up today but as we are going to run these in routine the process needs to be automated.
Always the same base mask: Y30I10I10
* Do NOT add a new sample sheet. Use the sample sheet created by the run (need to check exactly what it is called, but it's available directly in the run folder and is created by the iSeq software).
# TODO: doublecheck with @Emilia-Ottosson-Laakso if this is still True
the stats addition to cgstats is handled in us Clinical-Genomics/cgstats#20 or can be incorporated here if wanted
run folder on thalamus: /home/hiseq.clinical/iSeq/runs/ (as on thalamus)
demux folder on thalamus: /home/hiseq.clinical/iSeq/demux/ (as on thalamus)
use 1 mismatch allowed
Add cronjob to automatically start demux when run is finished.
Update 1161 Demultiplexing
Tolerances:
Can be started manually using CLI
documentation can be handled later
DoD:
script available for demultiplexing of iSeq runs similar to novaseq
cronjob running for automatic demultiplexing when run is finished
As a prod bioinfo member I want the iSeq runs to be demultiplexed automatically so that I don't have to spend time on manually starting the demultiplexing.
Problem: There is no procedure for demultiplexing of iSeq runs set up today but as we are going to run these in routine the process needs to be automated.
Suggested solution:
* Do NOT add a new sample sheet. Use the sample sheet created by the run (need to check exactly what it is called, but it's available directly in the run folder and is created by the iSeq software).# TODO: doublecheck with @Emilia-Ottosson-Laakso if this is still True/home/hiseq.clinical/iSeq/runs/(as on thalamus)/home/hiseq.clinical/iSeq/demux/(as on thalamus)Tolerances:
documentation can be handled laterDoD: