upstream: Align trim (#2)

* adding --min-depth flag to minion and parameterising the mask and stats calls with it

* parameterising the vcf filter with the same global min-depth variable for consistency

* adding github actions CI

* adding github actions CI

* adding github actions CI

* adding github actions CI

* moving unit tests over to github actions

* parameterising the vcf filter with the same global min-depth variable for consistency

* replacing travis with github action CI

* adding DOI to README

* updating artic-tools, adding more stats to artic report, running report regardless of strict, setting strict to filter VCF

* adding opt to enforce full length amplicon match during align trim, activate using --strict flag to minion

* tweaking report generator

* version bump

* docs update

* replacing longshot with the latest medaka

* trying to fix medaka install on osx

* adding bcftools norm command to remove vars from the pass VCF if they have been masked out in the preconsensus

* cleaner parsing of GQ field

* upgrading to latest medaka and dropping longshot from the conda env

* exposing opts for vcf_filter

* bumping medaka to latest patch

* unpinning pandas

* Change to overlap-based method of amplicon resolution

* Integrate new align_trim.py

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Co-authored-by: Will Rowe <[email protected]>
Co-authored-by: Chris Wright <[email protected]>