This PR removes the existing primer scheme files, which are a copy of the schemes here and replaces them with a git submodule.
This solves the following:
have a canonical scheme location instead of tracking/syncing multiple copies of the scheme across repos
includes the new primal scheme file format (*.primer.bed) which conforms to the BED standard
includes the new primal scheme files, such as amplicon insert coordinates (*.insert.bed)
However, this is PR introduces the following issues:
submodule would require explicit git clone --recursive in order to pull it. This is already included in the SOP but might not be in other places
the file path has changed (primer_schemes/nCoV-2019/V../ -> primer-schemes/SARS-CoV-2/V../, but the filename remains consistent (I will update the SOP if this PR gets approved)
This PR removes the existing primer scheme files, which are a copy of the schemes here and replaces them with a git submodule.
This solves the following:
*.primer.bed
) which conforms to the BED standard*.insert.bed
)However, this is PR introduces the following issues:
git clone --recursive
in order to pull it. This is already included in the SOP but might not be in other placesprimer_schemes/nCoV-2019/V../
->primer-schemes/SARS-CoV-2/V../
, but the filename remains consistent (I will update the SOP if this PR gets approved)This PR will close https://github.com/artic-network/artic-ncov2019/issues/12, https://github.com/connor-lab/ncov2019-artic-nf/issues/28, and makes https://github.com/artic-network/artic-ncov2019/pull/28 obsolete (sorry @m-bull)