Detect RNA-seq strandedness in FASTQ

[edsu7]

We need to run an alignment on our FASTQ files or a subset of them to determine the strandedness; need to add this check to our quite of seq-tools checks

[b-f-chan]

Suggestion: @edsu7 can you investigate Salmon to see if it can do this instead of us coding this into our scripts

https://salmon.readthedocs.io/en/latest/library_type.html#fragment-library-types

[b-f-chan]

Started this work, but encountered issues, may need to run on Linux not MacOS

[edsu7]

Based on below, it should take ~15 minutes for 600 million reads.

Posted into the wrong ticket.
Table removed

[b-f-chan]

Had to pull public data to be used; work ongoing

[b-f-chan]

On hold due to other priorities

[b-f-chan]

Targeting PR for this week

Some separate investigation required for NF-Core support

[b-f-chan]

Still low priority, leaving PR open until testing can be done

[puneet-oicr]

No new updates

[puneet-oicr]

No new updates