Closed ctr26 closed 3 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?
The routine globs for something like /*/V2/reference.fasta which has 3 hits in the submodu primer-schemes
git pull
should solve - this was fixed in the same commit as above.
My bad will try, has the nf-core been updated accordingly?
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...
As in cloning the repo and running main .nf
I.e.
nextflow run connor-lab/ncov2019-artic-nf ....
Vs
nextflow run main.nf
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
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