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wtsi-team112 / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019 - adapted to run at the Wellcome Sanger Institute
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Access schemeRepoURL locally #11

Closed sb10 closed 4 years ago

sb10 commented 4 years ago

To avoid any process needing an internet connection, and to minimise needless git clones, if https://github.com/artic-network/artic-ncov2019.git has been manually cloned locally, it should be possible to use that local clone path directly.

roamato commented 4 years ago

Need to check consistency though. The repo contains the primers info and that might get updated e.g. when new versions are released

sb10 commented 4 years ago

Is the current situation that you don't know what revision of artic-ncov2019.git was used in your analysis? I think knowing your revision (from on your own clone) for a whole run or multiple runs would be useful?

roamato commented 4 years ago

It gets recorded as part of the Nextflow execution. I like the suggesiton of making it explicit

sb10 commented 4 years ago

For a heavily productionized environment, it may be preferable to bypass the articDownloadScheme and makeIvarBedFile processes altogether and directly supply the full path to an ivar-compatible bed file and a reference file.

I think that's either an independent issue and solution, or it supercedes this approach and we don't bother merging PR #12.

sb10 commented 4 years ago

PR #12 merged