* Deprecate old tools and black format

* Support fragmented data

* use new trim primer arg in minion

* reverse the (revolting) primer position logic

* Fix find primer logic

* Improve the cursed report writer logic

* explicitly named function args, what a novel idea

* add temp debugging prints to find_primer

* Add logic to handle segments outside of primer scheme

* fix typo

* General bugfixes, test fix for overlapping variant issue

* add min mapq argument

* properly provide min_mapq to handle_segment

* Fix unmatched read group issue

* Fix 8 bit int error

* First attempt to integrate clair3 as optional
variant caller

* Slightly change env yaml format

* Specify env name in mamba gh action

* Checkout repo before installing env

* python 3.6.15

* Run on ubuntu 20.04

* unpin python

* Unpin python entirely

* Separate out tests

* correct unit test path

* remove retvar hints for compatibility

* Fix silly relative imports

* Switch to cyvcf and fix unit tests

* Fix pipeline parse unit test

* Fix fstring

* Large changes to make clair3 work, various unit test updates

* Fix fuzzy primer site match logic

* Fix minion_validator path

* Fix vcf merge bug with empty VCF files

* Increase fuzzy match default threshold to 20

* Fix CHROM bug in vcf merge properly

* Report failed workflow when variants are missed

* Fix vcf merge again

* Separate out tests

* No counter anymore

* Add C241T to SP1 variants

* Add limit on ref pileup

* Single copy of CVR1 12733 var

* re-enable other consensus tests

* First attempt to make minion validator less fragile

* Unify testvariants, improve test logic

* medaka has to be different smh

* Index ref fasta when using the clair3 workflow

* Add mean amplicon depth TSV output

* Update CLI and scheme fetcher

* Update align trim unit test

* Use proper version of V3 bedfile

* Fix pipeline unit test

* Fix align trim amp depth bug

* Call variants on non primertrimmed bam

* Don't test MT vs clair

* properly disable test

* Add docker build push action on release

* Grab wget in dockerfile

* Update docs and readme

* docker push on release only

* Remove debugging print statement

* Make fuzzy primer match logic clearer

* Install procps for nxf compatibility

* mods to Dockerfile

* wip

* update