This repository provides an example of using Nextflow with our tracking & observability tool - Tracer.

To install Tracer on your initialized Gitpod workspace:

--> Create your account on Tracer --> Copy & Paste one-line installation script at https://app.tracer.bio/app/setup

1. INDEX and QUANTIFICATION processes are run and tracked by Tracer
2. "nextflow run ./examples/example1.nf"

1. INDEX and QUANTIFICATION processes are run and tracked by Tracer using GEO E.coli dataset
2. Details of dataset available at "./examples/data/bacteria/datasets.txt"
3. "nextflow run ./examples/example2.nf"

1. INDEX and QUANTIFICATION processes are run and tracked by Tracer using GEO human AML dataset
2. Details of dataset available at "./examples/data/human/datasets.txt"
3. "nextflow run ./examples/example3.nf"

1. Generate a genome index and performs mapping of sample dataset using STAR

2. Details of dataset available at "./examples/data/human/datasets.txt"

3. "sh ./rnaseq/STAR.sh"

   Files

   • example1.nf, example2.nf, example3.nf : The main workflow script files.
   • index.nf: Contains the INDEX process definition [./examples/misc/]
   • quantpe.nf: Contains the QUANTIFICATION process definition. [./examples/misc/]

   Workspace

   • Conda and salmon are pre-configured in the workspace using docker.
   • Nextflow is pre-configured in the workspace using docker.
   • JAVA is pre-configured in the workspace using docker.
   • STAR is pre-configured in the workspace using docker.
   • Tracer: The tracking tool used in this workflow. Setup your Tracer account and record your unique API key at https://app.tracer.bio. Enter this one-line installation script prior to running other example scripts.

   Usage

   1. To clone the repository:

   git clone https://github.com/tracer-pod/utility-pod.git

   cd utility-pod

   Tracer Integration

   Tracer is integrated into the workflow to track the execution and versions of the processes. The workflow initiates Tracer at the beginning and terminates it at the end.

   License

   This project is licensed under the MIT License - see the LICENSE file for details.

   Acknowledgments

   • Thanks to the Nextflow community for their excellent documentation and support.

   GitPod

   

This README provides a comprehensive guide for users to understand and execute a nextflow RNA-Seq workflow with Tracer enabled tracking. Adjust the repository URL, license details, and acknowledgments as per your specific project details.