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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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articDownloadScheme isn't working with default URL #71

Closed ctr26 closed 3 years ago

ctr26 commented 4 years ago

The default URL leads to a git repo with a submodule which gets missed by a raw git clone, furthermore the code in articDownloadScheme will unintentionally collect from the symlinked sarscov2 folder and the ebola folder found there.

https://github.com/artic-network/artic-ncov2019.git https://github.com/artic-network/primer-schemes/tree/7d51020f7a4cf96d57d6aeb09bc4413e12ac9787

Best

Craig

m-bull commented 4 years ago

Hi @ctr26 - the default URL for articDownloadScheme points to https://github.com/artic-network/artic-ncov2019, which I think is the correct place - my tests at least pass using this URL! This was updated some four days ago though, so you might need a git pull to bring your local repo up to date with master.

Could you elaborate on the unintentional collection of the ebola scheme?

ctr26 commented 4 years ago

The routine globs for something like /*/V2/reference.fasta which has 3 hits in the submodu primer-schemes

https://github.com/artic-network/primer-schemes

received_236467337767896.jpeg

m-bull commented 4 years ago

git pull should solve - this was fixed in the same commit as above.

ctr26 commented 4 years ago

My bad will try, has the nf-core been updated accordingly?

m-bull commented 4 years ago

No problem - sorry this is repo is a bit of a moving target. Let me know how it goes with the updated version!

Can you elborate on the nf-core thing? Not quite sure what you mean...

ctr26 commented 4 years ago

As in cloning the repo and running main .nf

I.e.

nextflow run connor-lab/ncov2019-artic-nf ....

Vs

nextflow run main.nf

yockping commented 3 years ago

Hi, facing the similar problem and encounter error when execute the pipeline. Could please advise? Error as below:

Error executing process > 'ncovIllumina:prepareReferenceFiles:indexReference ([nCoV-2019.reference.fasta, ZaireEbola.reference.fasta, nCoV-2019.reference.fasta])'

Caused by: Process ncovIllumina:prepareReferenceFiles:indexReference input file name collision -- There are multiple input files for each of the following file names: nCoV-2019.reference.fasta

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh