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Clinical-Genomics / demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline
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Parse NIPT basemask from RunInfo.xml #96

Closed barrystokman closed 4 years ago

barrystokman commented 4 years ago

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.

barrystokman commented 4 years ago

PR: https://github.com/Clinical-Genomics/demultiplexing/pull/106

henrikstranneheim commented 4 years ago

Seems done - closing. Reopen if you disagree