qbicpipelines/sradownloader repository overview

⁠sradownloader

A pipeline to download raw data from SRA.

⁠Introduction

The pipeline is built using Nextflow⁠, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

⁠Quick Start

1. Install nextflow⁠

2. Install any of Docker⁠, Singularity⁠ or Podman⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort; see docs⁠)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run qbic-pipelines/sradownloader -profile test,<docker/singularity/conda/podman/institute>
   

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   Please check nf-core/configs⁠ to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

4. Start running your own analysis!

   nextflow run qbic-pipelines/sradownloader --run_acc_list '<path_to_acc_list.txt>' --ngc '<path_to_key.ngc>' -profile docker
   

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See usage docs⁠ for all of the available options when running the pipeline.

⁠Documentation

The nf-core/sradownloader pipeline comes with documentation about the pipeline: usage⁠ and output⁠.

⁠Credits

qbic-pipelines/sradownloader was originally written by Steffen Lemke⁠. Useful contributions by Susanne Jodoin⁠.

This pipeline was created with the nf-core⁠ template.

⁠Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines⁠.

⁠Citation

You can cite the nf-core publication as follows: