New HPC Updates

[kew24]

This PR is comprised of updates to run this pipeline on VAI's new HPC. The following changes due to HPC differences are outlined here:

• pbs -> slurm directives, variables, and commands
• bbc -> bb2 modules
• update log names based on wildcards (following other BBC slurm-based workflows)

Plus, a few general updates:

• more info in README to clarify user instructions
• update the listed genome reference file to newer version
• update rulegraph image to include all rules in this pipeline

I'm happy to rework anything as needed – just let me know if you want me to change anything,. Otherwise, feel free to squash & merge (or just merge) this pull request. Thanks!

[kew24]

Thanks for your comments, @genomics-kl! I just removed the unnecessary >&1 from those echos in my most recent commit. I also checked the pipeline outputs compared to the c. elegans data you had run this on previously, and it looks like there are slight differences in:

• samblaster & FastQC numbers (small change in number of duplicates, I'm guessing this is due to updates between versions of the software used in our modules?)
• slight changes in PL in the vcf (not sure why there's a difference -- I should be using the same gatk version [4.1.8.1]) e.g.,

  26c26
  < I     134913  .       A       C       462.15  PASS    GT:AD:DP:GQ:PGT:PID:PL:PS       0/0:48,0:48:0:.:.:0,0,1287:.    0/0:35,0:35:0:.:.:0,0,903:.     0/0:56,0:56:17:.:.:0,17,2050:.  0/0:54,0:54:0:.:.:0,0,1617:. 0/0:62,0:62:0:.:.:0,0,1867:.    0/0:44,0:44:0:.:.:0,0,1417:.    0/0:48,0:48:0:.:.:0,0,1157:.    0|1:36,10:46:99:0|1:134913_A_C:312,0,1482:134913        0/0:48,0:48:0:.:.:0,0,1414:.    0|1:47,7:54:99:0|1:134913_A_C:152,0,1952:134913      0/0:61,0:61:0:.:.:0,0,1762:.    0/0:47,0:47:0:.:.:0,0,1204:.    0/0:46,0:46:0:.:.:0,0,1436:.
  ---
  > I     134913  .       A       C       462.15  PASS    GT:AD:DP:GQ:PGT:PID:PL:PS       0/0:48,0:48:0:.:.:0,0,1287:.    0/0:35,0:35:0:.:.:0,0,903:.     0/0:56,0:56:17:.:.:0,17,2049:.  0/0:54,0:54:0:.:.:0,0,1617:. 0/0:62,0:62:0:.:.:0,0,1867:.    0/0:44,0:44:0:.:.:0,0,1417:.    0/0:48,0:48:0:.:.:0,0,1157:.    0|1:36,10:46:99:0|1:134913_A_C:312,0,1482:134913        0/0:48,0:48:0:.:.:0,0,1414:.    0|1:47,7:54:99:0|1:134913_A_C:152,0,1952:134913      0/0:61,0:61:0:.:.:0,0,1762:.    0/0:47,0:47:0:.:.:0,0,1204:.    0/0:46,0:46:0:.:.:0,0,1436:.

Overall, the majority of our results look the same (via multiQC & querying the final snpEff vcf). If we're ok w/ the differences I've outlined above plus some slight differences in the way the logs directories are structured, we should be good to merge. Let me know if you want me to look into anything more intensively before we just accept this into main, though.