ToDo list for next update

[TCLamnidis]

nf-core/eager prep:

• Swap to using pandora2eager instead of its predecessor. This mostly updates the pickup of strandedness, udg treatment, and colour chemistry for newer protocols/sequencers.
• Change reverse adapter for ssDNA PE data.

Poseidon packages:

• collecting ssDNA and dsDNA genotypes in each package (there should be no clashing sample IDs anymore) (Single stranded sample name change in eager processing #8)
  • Collecting the genotypes for poseidon package creation
  • Janno fill-in for both versions
• Bump created packages to Poseidon version 2.7.0 (currently still 2.5.0)

PDF Reports:

• BUG: Currently, only info for TF and SG are kept in the run table. Keep RP/RM as well for future reports.
• Update report to pull info from janno files instead of pandora. This is a leftover from before the jannos were automatically filled in, and no longer necessary.
• Remove Arch IDs from Read table (READ table improvement in automated report #12)
• Add a map of the sites to the title page.
• Add lexicon to reports (Add lexicon to PDF reports #11)
• Update list of people mentioned in the reports (People in named in the report #14)
• Update PCA plots to deal with over-plotting (Change PCA plotting #16)
• Add skeletal element to sequencing table (Add skeletal element sampled in the Table of sequencing results #18)
• Optional: Table of skeletal elements we have per individual #17
• Optional: Turn R Notebook into a fully-embedded HTML? #15

Phenotypic SNPs:

• Corrections/Extension to Phenotypic SNP annotations #10 : Some fixes were already done, but proper curation of a SNP list was never my intention, so I will not be extending the list for now.

Processing:

• Have each eager run start from a stable, unique directory for stable resuming.
• Allow parallelisation of eager jobs (From serialisation to parallelisation #6)

[TCLamnidis]

Using pandora2eager for TSV preparation actually revealed a small bug. The previous approach required some manual tweaks for certain samples, and hence some Sample_IDs did not get the appropriate suffix. This is not an issue until genotypes are collected together, but might require some slight reprocessing to fix properly.

UPDATE:
Upon further inspection, the only batches where there is a mix of dsDNS and ssDNA data, and suffixes were accidentally skipped are:
2023-11-07-bulgaria
2021-01-04-austria
In both cases, the individuals that missed the suffix did not have a dsDNA equivalent, and hence no results were lost/hidden, just the naming was inconsistent in the resulting poseidon packages.

This means that no reprocessing will be necessary to merge dsDNA and ssDNA genotypes in the new poseidon packages!

[stschiff]

OK, but just to clarify: You did not fix the _ss suffix where they were missing now? I think that's OK, just want to be sure.

[TCLamnidis]

I had not, until now.
Both of the aforementioned batches needed reprocessing to fix ssDNA/PE adapter leftovers, so I took the opportunity to also fix the suffixes for them.