README.md

About SciPipe

SciPipe is a workflow library implemented as a programming library in Go. See scipipe.org for more information!

Training material and documentation

• Link to tutorial
• Link to online documentation
• A basic tutorial as a screencast
• Case study workflows for the SciPipe paper

Community-developed workflows in SciPipe

• "Reproducible Probabilistic Target Profiles"
  • Repository: https://github.com/pharmbio/ptp-project
  • Description: A workflow developed by the workflow tool authors, for building target binding profiles, using QSAR and SVM (see the paper for more details).
• Kleuren SciPipe workflow
  • Repository: https://github.com/Colelyman/kleuren-scipipe-workflow
  • Description: A scipipe workflow for building the necessary data structures for running kleuren.

Running the proof of concept SciPipe pipeline

1. Install the Go toolchain by following this page for the specific instructions for your operating system.
   • Note that on Windows, you need to have a POSIX-compliant bash environment to run Scipipe, such as Windows Subsystem for Linux (WSL). Find more information about installing WSL here
2. Go into the scipipe directory:

   cd scipipe

3. Run the workflow using the run.sh bash script:

   ./run.sh

   Alternatively you can run the full command directly:

   go run example.go -ref ../test_data/transcriptome.fa -left ../test_data/reads_1.fq.gz -right ../test_data/reads_2.fq.gz -outdir results

Done!

Notes and Contribution

This pipeline is a minimal example of using SciPipe. We welcome contributions to the documentation and workflow, please create an issue or submit a pull request!

How to cite SciPipe

Please cite SciPipe as:

Lampa, S., Dahlö, M., Alvarsson, J., & Spjuth, O. (2019). SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines. GigaScience, 8(5), giz044. DOI: 10.1093/gigascience/giz044