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connor-lab / 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
GNU Affero General Public License v3.0
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Synching with fieldbioinformatics #38

Closed jts closed 4 years ago

jts commented 4 years ago

Hi,

I noticed the environments are out of synch with the main fieldbioinformatics env (which has merged the nanopolish and medaka environments). Nanopolish has been updated a few times since 0.12.5 too and I'd like this repo to use the latest version. I don't mind sending a PR here when I update nanopolish but I'd prefer if I could just update fieldbioinformatics and have it propagate here - is this possible to set up?

Thanks, Jared

jts commented 4 years ago

Great, thank you!

On Apr 26, 2020, at 9:42 AM, Matt Bull notifications@github.com wrote:

 Hi @jts - I've literally been working on this this afternoon, will update to follow fieldbioinformatics master again which should propagate your PRs this way.

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m-bull commented 4 years ago

Deleted message above - I'll think of a cleverer way to grab the environment.yml files from fieldbioinformatics and push some updates this afternoon.

m-bull commented 4 years ago

Hi @jts - this took me longer than anticipated!

Because I need to pull in the fieldbioinformatics tools as a dependency, there's no simple way to do that from environment.yml in the fieldbioinformatics repo, as its not listed as a dependency of itself.

I've compromised on updating the Nanopore conda environment on the fly using environment.yml from https://github.com/artic-network/artic-ncov2019, as this is the environment/process described in the ARTIC SOP, which I wanted to follow as closely as I could with this workflow. This environment pulls in all of the dependencies required for the fieldbioinformatics/artic tools, and fieldbioinfomatics itself, which covers everything the workflow needs. Hope this is acceptable!

Specific changes supporting this are in https://github.com/connor-lab/ncov2019-artic-nf/pull/39/commits/3a39f9c74f4bd9da57ad5cd46f48d240e81cb8c9.

jts commented 4 years ago

Thanks @m-bull, that looks good. Just to make sure I understand correctly, will it update environment.yaml every time nextflow is run?

If possible could you make the default nanopolish 0.13.2 anyway? I'll be making a PR against artic-ncov-2019 today.

m-bull commented 4 years ago

@jts - final comment on this, and properly fixed with https://github.com/connor-lab/ncov2019-artic-nf/commit/8b0f5ea06f94a8f7235613c20fc371c886f695b9.

This uses the artic package directly from conda, so will pull in whatever deps are defined there.