Merge branch 'new-neb-scheme' into 'dev'

ALT vs alt

See merge request epi2melabs/workflow-containers/wf-artic!111

CHANGELOG.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [unreleased]
 ### Added
 - `--pangolin_options` command line arg, use with quotes i.e.: "--analysis-mode fast"
-- NEB VarSkip V2b
+- NEB VarSkip V2b primer scheme added
 ### Changes
 - Better help text on cli
 

data/primer_schemes/SARS-CoV-2/NEB-VarSkip/v2b/SARS-CoV-2.scheme.bed

@@ -96,7 +96,7 @@ MN908947.3	19098	19125	nCoV-2019_48_LEFT	2
 MN908947.3	19623	19655	nCoV-2019_48_RIGHT	2
 MN908947.3	19488	19515	nCoV-2019_49_LEFT	1
 MN908947.3	20037	20064	nCoV-2019_49_RIGHT	1
-MN908947.3	20010	20038	nCoV-2019_49_RIGHT_ALT1	1
+MN908947.3	20010	20038	nCoV-2019_49_RIGHT_alt1	1
 MN908947.3	19885	19911	nCoV-2019_50_LEFT	2
 MN908947.3	20462	20484	nCoV-2019_50_RIGHT	2
 MN908947.3	20340	20366	nCoV-2019_51_LEFT	1
@@ -111,7 +111,7 @@ MN908947.3	21926	21955	nCoV-2019_55_LEFT	1
 MN908947.3	22480	22510	nCoV-2019_55_RIGHT	1
 MN908947.3	22347	22373	nCoV-2019_56_LEFT	2
 MN908947.3	22853	22877	nCoV-2019_56_RIGHT	2
-MN908947.3	22742	22773	nCoV-2019_57_LEFT_ALT2	1
+MN908947.3	22742	22773	nCoV-2019_57_LEFT_alt2	1
 MN908947.3	22749	22776	nCoV-2019_57_LEFT	1
 MN908947.3	23288	23310	nCoV-2019_57_RIGHT	1
 MN908947.3	23122	23144	nCoV-2019_58_LEFT	2