Skip to content

This is a workflow that allows you to download whole projects and metadata with kingfisher. Additionally, it takes care about merging same samples together.

License

Notifications You must be signed in to change notification settings

metagenome-atlas/kingfisher_workflow

 
 

Repository files navigation

Snakemake workflow: Kingfisher_workflow

Snakemake GitHub actions status

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.

Usage

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

TODO

  • 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.

About

This is a workflow that allows you to download whole projects and metadata with kingfisher. Additionally, it takes care about merging same samples together.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • Python 100.0%