A demo workflow showing download, extraction, and compression of sequences from SRA.
This branch is intended to be used with the Docker profile.
A directory is mounted as the container's /tmp directory. You can significantly improve the performance of fasterq-dump if the mounted directory (provided as params.scratch_space) is either on an SSD or even better an in-memory tmpfs.
The workflow generates an execution timeline giving a rough idea of the performance. You can find a sample execution timeline report in info/execution_timeline.html.
- Set up nextflow as described here.
- If you didn't run this pipeline in a while, possibly update nextflow itself.
nextflow self-update - Then run the pipeline.
nextflow run main.nf -profile docker --scratch_space=/your/own/path
- Copyright © 2020, Unseen Bio ApS.
- Free software distributed under the GNU Affero General Public License version 3 or later (AGPL-3.0-or-later).