…ling issue

fixed typos

* starting locidex database integrations

* updated added new files

* updated locidex db identification

* updated automated allele selection

* updated todos

* added test data for locidex databases, tests should still function:

* updated nextflow schema.json

* Removed tests for comparing updates for old and new locidex profiles

Perhaps the relevant fields should be sub set out

* removed dead test file

* updated test profile

* restrucutured file staging for locidex select

* started creation of real tests for locidex workflow

* updated locidex test data

* updated locidex workflow and tests

* updated docker container

* addressed PR issues, still more work to be done

* updated database selection functions to get an optimal match

* added skipped allele calling to test config

* updated test conditions

* updated test files

* updated locidex select paths

* removed trailing whitespace

* updated tests to include passing cases

* added locidex summary process

* updated fixe issues with integer sizing

* debugging summary test

* Added field for reportable alleles

* updated reportable loci test

* updated locidex summary tests

* updated missing allelels JSON type

* upated not database selected output

* updated IRIDANEXT config for locidex values

* updated locidex end-to-end tests

* updated locations of locidex test

* zipped and updated sample datasets

* upated locidex end to end tests

* fixed typos in change log

* updated locidex tests

* cleaned up datebase name parsing

* fixed code comment

* updated code comments

* made updates on PR comments

* normalized output for iridanext across allele scheme input options

* updated test cases

* updated locidex_select tests to match updated interface

* updated test to work in github actions

* removed sneaky todo

* updating issues identified and regression in kraken2 header parsing

* reverted zipped file handling

* fixed regression locidex select

* removed repeated variables

* updated staging of report input to locidex summarize

* updated file parsing in locidex summarize

Thank you Aaron!

* updated changelog

* extracted inline code in function

* bumped locidex container

* updated final todos

* updated options to locidex_select test to terminate processes on failure

…LST (#98)

* updated Torsteins mlst container, as results were differing with PubMLST

* updated wordslist

* updated test to use e.coli achtman 4

* update listeria scheme selection

* updated changelog statement

#102)

* updated tests running average coverage calculations in cloud executors

* committing progress, difference in behaviour between nextflow versions is being observed

* fixed missing coverage value in version 24 of nextflow

* updated test ouputs

* removed docker.userEmulation as marked as deprecated

* renamed duplicated test name

…ault container option

dropped quay.io from docker paths

* fixed typo and metagenomic QCSummary message

* updated changelog

* removed comma

* updated metagenomic tests

* added missing test files

* updated virus mash sketch

* updated output values

* fixed test typo

* reintegrated deleted test

* updated config defaults for various organisms

* updated changelog

* updated parameters for allele schema

* updated changelog

* fixed error in parameter updates

* fixed misspelled param

* updated test config

* updated CLI argument

* dropped allele scheme used from the irida-next config

* updated tests to pass

* updated container default settings

* updated changelog and version