A Snakemake workflow for downloading whole projects together with their metadata using kingfisher-download. It extends its functionality by making possible to download samples from the same BioProject in parallel. Additionally, it merges runs coming from one sample together, to make further analysis easier.
The usage of this workflow is described in the Snakemake Workflow Catalog.
you need to install snakemake.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) sitory and its DOI (see above).
Run as
snakemake -d output_dir -j1 separate_samples --config BioProject=PRJNA363003 --use-conda --resources ncbi_connection=4
Run as
snakemake -d output_dir -j10 --config BioProject=PRJNA363003 --use-conda --resources ncbi_connections=4
- Replace
<owner>and<repo>everywhere in the template (also under .github/workflows) with the correct<repo>name and owning user or organization. - The workflow will occur in the snakemake-workflow-catalog once it has been made public. Then the link under "Usage" will point to the usage instructions if
<owner>and<repo>were correctly set.