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

i. Install nextflow

ii. Install either Docker or Singularity for full pipeline reproducibility (please only use Conda as a last resort; see docs)

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

nextflow run -r master steffenlem/sradownloader -profile test,<docker/singularity/conda/institute>

iv. Start running your own analysis!

nextflow run -r master steffenlem/sradownloader --run_acc_list '<path_to_acc_list.txt>' --ngc '<path_to_key.ngc>' -profile docker

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

Documentation

The steffenlem/sradownloader pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Credits

steffenlem/sradownloader was originally written by Steffen Lemke.

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:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
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