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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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PR to add a new primer scheme? #81

Open bwlang opened 2 years ago

bwlang commented 2 years ago

I've been hearing questions from people who would like to use the new NEB VarSkip primer scheme with this workflow.

I can get things working if I suggest that people download a custom scheme directory and call a command like this:

artic minion --strict  --threads 8 --read-file reads.fastq --scheme-directory schemes --scheme-version 1a NEB_VarSkip reads  --skip-nanopolish --medaka --medaka-model r941_min_fast_g303

with a custom scheme structure like this:

schemes/NEB_VarSkip/V1a
schemes/NEB_VarSkip/V1a/NEB_VarSkip.scheme.bed
schemes/NEB_VarSkip/V1a/NEB_VarSkip.reference.fasta
schemes/NEB_VarSkip/V1a/NEB_VarSkip.reference.fasta.fai

I'd like to submit a PR to this repository that would allow simpler operation and avoid requiring people to download and organize a scheme directory.

artic minion --strict  --threads 8 --read-file reads.fastq NEB_VarSkip reads  --skip-nanopolish --medaka --medaka-model r941_min_fast_g303

This doesn't match very well with your naming hierarchy which expects a nCoV-2019 directory, and a simple numeric version selector.

What's the best path forward here? allow string version numbers to artic-tools so I can add something like this

schemes/nCoV-2019
schemes/nCoV-2019/VNEB-VarSkip-1a
schemes/nCoV-2019/VNEB-VarSkip-1a/nCoV-2019.reference.fasta.fai
schemes/nCoV-2019/VNEB-VarSkip-1a/nCoV-2019.reference.fasta
schemes/nCoV-2019/VNEB-VarSkip-1a/nCoV-2019.scheme.bed

or maybe break out of the organism based organization?

EpiDemos82 commented 2 years ago

Bump... we would like this functionality as well. Thank you!

bwlang commented 2 years ago

@nickloman: any chance you can advise on how to proceed?