Add multi-ref scheme selection support #140
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* 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
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