add optional task for shigeifinder w/ reads as input; update default docker for both shigeifinder & shigatyper

[kapsakcj]

Setting as a draft until the staphb/shigeifinder:1.3.3 docker image is available

Ready for review!

Summary of code changes in PR:

• updates default shigatyper docker image to staphb/shigatyper:2.0.3 (tiny bug fix) from 2.0.2
• updates default shigeifinder docker image to staphb/shigeifinder:1.3.3 (adds single end support) from 1.3.2
  • This docker image is currently not available on dockerhub/quay, but will be added very soon
• adds new task for running ShigEiFinder on reads as input (previous task uses assembly as input). Compatible with PE and SE Illumina data
  • ShigEiFinder on reads task is OFF by default but can be turned on by setting the merlin_magic workflow boolean input call_shigeifinder_reads_input to true
• This new task has been added to both PE & SE TheiaProk workflows, and adds 10 new output columns. These columns are identical to the task that uses assembly as input, but the column headers have the suffix _reads to differentiate between the 2 tasks.
• These outputs have been added to export_taxon_table task and this runs as expected too 👍

testing

I have tested both PE and SE samples on >100 Shigella & E. coli samples in Terra and they have ran as expected. TheiaProk_PE test on various Shigella and a few EIEC's TheiaProk_SE test on various Shigella and a few EIEC's. Can ignore the 1 failure as it's related to shigatyper and not shigeifinder TheiaProk_PE test on 73 E. coli

[kevinlibuit]

Everything looking solid. Running one more test with default merlin magic params ( (i.e. call_shigeifinder_reads_input = false) for sanity's sake.

Will merge pending a successful run.