Cleanup Code and Improvements for Release 2.0.0 (#93)

* adjust config spacing, param location and resources, remove some unused params

* initial cleanup

* Remove illumina specific workflows and params

* bump required nf version

* remove bam-to-cram module, adjust resources

* adjust how main handles input directory for both flat and barcoded inputs

* initial pass to remove duplicate work, fix formatting, and improve flow

* fix missed variable changes

* fix other missed spots with tuples

* fix to failing sample reporting

* remove unneeded module, adjust guppyplex output

* fix naming and empty file tracking for medaka

* initial qc adjustments to match other medaka changes

* Adding better function definitions to python functions (#94)

* fix wrong brackets for barcode regex

* rework scheme implementation

* adjust ncov-tools to allow different prefixs

* update help and config to match

* adjust git ci test scripts

* remove previous test files that are not run

* add a second sample for tests

* remove additional ci test files, unneeded

* fix schemes

* adjust schemes validation

* make aligned file optional

* adjust metadata input for ncov-tools fixing missing file

* small test adjustment

* fix up scheme input validation

* add in initial nextclade implementation

* fix up process tracking

* add version tracking to where it was missing

* adjust module formatting

* consistent module variable formatting

* removal of duplicate checks, fix upload of fast5s

* fix nml config, add in nc results correction to qc

* adjust qc script for fs flags

* remove nextflow_qc_pass column and adjust the tracking

* Switch to all snake_case params. Add readme updates and changelog

* add medaka model to version tracking

* final adjustments with schemes and steps

* add a bit more info to the changelog

.github/data/metadata.tsv

@@ -1,2 +1,2 @@
 sample	run	barcode	project_id	ct	date
-TestSample1	Test1	78	2349	Undetermined	2022-09-10
+TestSample1	Test1	78	2349	23	2022-09-10