Display sequencing metadata from the run_dir

[matrulda]

Description of feature

It would be nice if metadata regarding the sequencing run was displayed in the reports. In the case of an Illumina run this could include:

• Control software version
• Reagent kit version
• RTA version
• Flowcell type
• and more...

This should be data that can be scraped from sequencing output files, like RunInfo.xml and RunParameters.xml.

This information could be shown in its own section in the reports or be part of the Software versions table.

This is how this feature has been implemented in seqreports: https://github.com/Molmed/seqreports/blob/main/bin/get_metadata.py

[mahesh-panchal]

A possible method that might help with speed is to implement this natively in Groovy. Processes using exec are executed on the head node and don't need to be distributed to a node like a python script does.

The XML slurper lib should make it easy-ish to parse out the relevant meta data and add it to the meta map.
https://groovy-lang.org/processing-xml.html#_simply_traversing_the_tree

[matrulda]

Good point, something to keep in mind.

[FranBonath]

This won't be part of V1, but we very much would like this in later versions. Adding it to the Hackathon page.

[matrulda]

What do we need:

• Function to use the run_dir to determine the seq platform (Alternatively a parameter from seq platform)
• Parser functions for the seq platforms (start with Illumina and Nanopore)

Some things to keep in mind:

• Each input samplesheet can contain multiple run directories. And tags might group samples across multiple run directories together.

We will start by implementing the parser functions.