When demultiplexing NIPT runs form the NovaSeq
I want the basemask to be derived from RunInfo.xml
so that the demultiplexing automation can pick up both regular and NIPT runs.
Problem description:
Currently, when the automation picks up a run ready to be demultiplexed on thalamus, the script demux-novaseq.bash uses a hardcoded basemask Y151I10I10Y151. NIPT runs however use a basemask of Y51I8I8Y51. The basemask information for a NIPT run is stored in the RunInfo.xml and can be parsed form there.
See /home/hiseq.clinical/STAGE/novaseq/runs/200326_A00689_0120_AHHV7KDRXX on thalamus for examples.
Suggested solution:
Parse the basemask from RunInfo.xml. Demultiplexing on hasta uses the function get_basemask() in /home/proj/production/bin/git/demultiplexing/scripts/demux.functions, perhaps this can be used as an example.
Requirements:
1) Automation can start demultiplexing of NIPT runs automatically with the correct basemask.
When demultiplexing NIPT runs form the NovaSeq I want the basemask to be derived from RunInfo.xml so that the demultiplexing automation can pick up both regular and NIPT runs.
Problem description:
Currently, when the automation picks up a run ready to be demultiplexed on thalamus, the script
demux-novaseq.bash
uses a hardcoded basemaskY151I10I10Y151
. NIPT runs however use a basemask ofY51I8I8Y51
. The basemask information for a NIPT run is stored in the RunInfo.xml and can be parsed form there.See
/home/hiseq.clinical/STAGE/novaseq/runs/200326_A00689_0120_AHHV7KDRXX
onthalamus
for examples.Suggested solution:
Parse the basemask from RunInfo.xml. Demultiplexing on hasta uses the function
get_basemask()
in/home/proj/production/bin/git/demultiplexing/scripts/demux.functions
, perhaps this can be used as an example.Requirements:
1) Automation can start demultiplexing of NIPT runs automatically with the correct basemask.