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naobservatory / mgs-pipeline

MIT License
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Add Lagenfeld 2022 #20

Closed dp-rice closed 9 months ago

dp-rice commented 9 months ago

Paper: https://www.biorxiv.org/content/10.1101/2022.07.08.499345v2.full Accession: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA853368

Got sample metadata using the SRA run selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA853368&o=acc_s%3Aa (and excluding the Oxford Nanopore samples).

Note: ./import-accession.sh gave errors when trying to download the Oxford Nanopore samples (because there aren't fastq files). I don't think this caused any downstream problems, but it does mean there are some empty objects in the S3 bucket.

dp-rice commented 9 months ago

Running the pipeline now. Will probably take overnight.