Fetch read length info for run instead of just lane 1

[kjellinjonas]

Description:

Previously, get_metadata.py reported the read and index length based on the information from lane 1 which could be misleading in some cases. Therefore, it was decided that the script should be updated so that it shows the read length setting for the run instead.
In this update, this is achieved by fetching length information from RunInfo.xml

Also updated actions/cache from v2 --> v4.2.2 to enable automatic testing

Risk analysis:

The scripts will most likely fail if there are updates to the structure of the RunInfo.xml file. However, the damage from this would be minimal and should be noticed immediately.

Validation procedure:

Run ngi work flow, generate reports and makes sure that the expected read and index lengths are printed in the report.

[nkongenelly]

Great and neat work! This looks good to me.

I would like to ask @matrulda for a second review just incase I might have missed anything i the bioinformatics side.

[matrulda]

Looks good! Left two suggestions for you.

[matrulda]

Great, looks good!

An unrelated thing that I noticed: When running the pipeline we display a version number that has not been updated in 2 years. The reason for this is that we no longer create releases for this pipeline and instead just point to commits. Since this pipeline is run through the sequencing-report-service, it became too much of a hassle to create two releases for one update.

Back to the point: until we find a way to display the commit, I think we should remove this line

seqreports/main.nf

Line 70 in a981694

printVersion()

and the function that is used.

It is out of scope for this ticket, so let me know if you rather not address it and I can make a ticket about it instead.

[matrulda]

Awesome, thank you!