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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Update nextclade #70

Closed sofstam closed 1 year ago

sofstam commented 1 year ago

The purpose of the code changes are as follows:

Please note that in order to be in production sofsta has to change to genomicmedicinesweden

Standard test procedure

This version is a:

sofstam commented 1 year ago

@JD2112 Could you maybe test that this works locally for you? Or anyone else that could help us with that? @pbiology The containers in cg are updated every Friday at 04.00 and we need to sync with prod-bioinfo before this PR is merged.

JD2112 commented 1 year ago

@JD2112 Could you maybe test that this works locally for you? Or anyone else that could help us with that? @pbiology The containers in cg are updated every Friday at 04.00 and we need to sync with prod-bioinfo before this PR is merged.

@sofstam Can't test locally. "access to the resource is denied". Caused by: Failed to pull singularity image command: singularity pull --name sofsta-gms-artic-pangolin-latest.img.pulling.1666286780351 docker://sofsta/gms-artic-pangolin:latest > /dev/null status : 255 message: FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://sofsta/gms-artic-pangolin:latest: reading manifest latest in docker.io/sofsta/gms-artic-pangolin: errors: denied: requested access to the resource is denied unauthorized: authentication required

sofstam commented 1 year ago

@JD2112 Thank you! Shall I maybe build the container under genomicmedicinesweden and when the PR is tested locally, re-run the default github actions?

JD2112 commented 1 year ago

@sofstam Sure...or just change the ownership of your Docker container :)

JD2112 commented 1 year ago

@sofstam #70 new nextclade cli: 'typing.nf' nextclade run \ --input-dataset data/sars-cov-2 \ --output-tree ${sampleName}_tree.json \ --output-tsv ${sampleName}.tsv \ --output-json ${sampleName}.json \ ${consensus_fasta}

sofstam commented 1 year ago

@pbiology This PR is ready for merging.

pbiology commented 1 year ago

As soon as the checks are resolved I'd go for it