Fix #237: Upgrade Skesa container to 2.5.1 to fix ownership issue with /tmp

[samuell]

Description

See #237

This PR fixes #237 by upgrading the Skesa container to version 2.5.1.

Primary function of PR

• Hotfix
• Minor functionality improvement
• Major functionality improvement / New type of analysis
• Backward-breaking functionality

Testing

• Have been running the full staphylococcu_aureus workflow on 5 samples of real data, up until running into No such command 'create-cdm-input', in prp #243

Sign-offs

• Code reviewed by @octocat
• Code tested by @octocat

[samuell]

Just noting this conversation from Slack:

Ryan James Kennedy 6 hours ago
We need test samples for all the species we run to check that updates of software work across the board. Is that possible to organise @ Isak Sylvin

Isak Sylvin 6 hours ago
Sitting in another meet so bit distracted.
But yea it shouldnt be hard to organise. Could just saw down existing MRSA samples to mini dataset. Could even share it publicly on github at that point

[ryanjameskennedy]

@mhkc where did you find those test reads for tb? Or did you just simulate reads from the reference genome? (wgsim is a good tool for this btw)?

[mhkc]

I just took public samples from EBI with annotated as being antibiotic resistant and with good sequencing depth.

[samuell]

Have been testing now on some resistant Klebsiella data:

The following are correctly typed as carbapenem resistant by both resfinder and amrfinder:

• https://www.ebi.ac.uk/ena/browser/view/SRR12149874
• https://www.ebi.ac.uk/ena/browser/view/SRR12149876
• https://www.ebi.ac.uk/ena/browser/view/SRR4191406
• https://www.ebi.ac.uk/ena/browser/view/SRR4191407
• https://www.ebi.ac.uk/ena/browser/view/SRR4191408
• https://www.ebi.ac.uk/ena/browser/view/SRR4191409
• https://www.ebi.ac.uk/ena/browser/view/SRR4191411

The following is resistant according to amrfinder, susceptible according to resfinder:

• https://www.ebi.ac.uk/ena/browser/view/SRR4191410

These strains are supposed to be colistin resistant (according to description), but is only typed as susceptible by resfinder (no colistin from amrfinder):

• https://www.ebi.ac.uk/ena/browser/view/SRR15293794
• https://www.ebi.ac.uk/ena/browser/view/SRR3174988

These are supposed to be meropenem resistant, but only typed as susceptible by resfinder (no typing by amrfinder):

• https://www.ebi.ac.uk/ena/browser/view/SRR8603248

Supposed to be resistant to silver nanoformulations, typed as silver resistant by amrfinder:

• https://www.ebi.ac.uk/ena/browser/view/SRR9733701
• https://www.ebi.ac.uk/ena/browser/view/SRR9733703
• https://www.ebi.ac.uk/ena/browser/view/SRR9733704

Any comments on this @mhkc @ryanjameskennedy ? Is this testing procedure sufficient, and are the results acceptable? Otherwise, do you have suggestions for other things to try?