Merge pull request jts#91 from jts/fix_ref_fasta_index

Add reference indexing, support different primer name prefixes

Merge pull request jts#84 from jts/fix_report_column_width

fixed Flagged Samples Pangolin Notes column width

Merge pull request jts#83 from jts/add_scorpio

fixed column error from scorpio_call addition

Merge pull request jts#80 from fmaguire/add_configurable_outputdir

Add configurable optional output directory

Merge pull request jts#75 from jts/fix_snpeff_build

snpEff database build support for different version

Merge pull request jts#73 from jts/snpeff_nolog

added -noLog option to snpEff

Merge branch 'add_lineage' of https://github.com/jts/ncov-tools into …

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Merge pull request jts#58 from dfornika/patch-1

Fix conda package name for parasail

remove non-required config options from example

Merge pull request jts#54 from jts/remove_ncov_parser_add_po_pr

Removed parser package from repo, added pip install ncov-parser, includes PO PR 53