Nextflow Tracer Use-Case Example

This repository provides an example of using Nextflow with a tracking tool called Tracer. The workflow consists of three main files: main2.nf, index.nf, and quantpe.nf. The key workflow file is main2.nf.

Overview

The workflow performs the following steps:

1. Initializes the Tracer tool.
2. Executes the INDEX process to prepare the transcriptome.
3. Executes the QUANTIFICATION process to quantify the paired-end reads.
4. Terminates the Tracer tool.

The user can run the entire workflow by typing nextflow run main2.nf.

Files

• main2.nf: The main workflow script.
• index.nf: Contains the INDEX process definition.
• quantpe.nf: Contains the QUANTIFICATION process definition.

Requirements

• Conda and Salmon: Anaconda will be auto-installed along with salmon when you initialise your GitPod workspace.
• Nextflow: Nextflow will be auto-installed on your GitPod workspace
• 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 API key when prompted for Tracer installation. Exit terminal & Open a new terminal to initiate Tracer.

Usage

1. Clone the repository:

   bash git clone https://github.com/yourusername/your-repo-name.git cd your-repo-name

2. Input data:

   • Input files gut_1.fq and gut_2.fq are present in the data/ggal/ directory.
   • Transcriptome reference is placed in the data/ggal/ directory and is named ref1.fa.

3. Workflow will be auto-run upon initiating a new terminal post Tracer installation using the following command:

   nextflow run main2.nf

Workflow Details

main2.nf

This file contains the main workflow definition:

'groovy' nextflow.enable.dsl=2

params.reads = "$projectDir/data/ggal/gut_{1,2}.fq" params.transcriptome = "$projectDir/data/ggal/ref1.fa"

// Include the INDEX process include { INDEX } from './index.nf'

// Include the QUANTIFICATION process include { QUANTIFICATION } from './quantpe.nf'

workflow { // Create a channel from the reads read_pairs_ch = Channel.fromFilePairs(params.reads, checkIfExists: true)

// Run the INDEX process
index_ch = INDEX(params.transcriptome)

// Run the QUANTIFICATION process
quant_ch = QUANTIFICATION(index_ch, read_pairs_ch)

}

index.nf

Defines the INDEX process that builds an index from the transcriptome reference:

'groovy' nextflow.enable.dsl=2

/*

• Define the INDEX process */ process INDEX { input: path transcriptome

  output: path 'salmon_index'

  script: """ tracer start tracer tool index v1 salmon index --threads ${task.cpus} -t ${transcriptome} -i salmon_index """ }

quantpe.nf

Defines the QUANTIFICATION process that quantifies the paired-end reads using the index:

'groovy' nextflow.enable.dsl=2

/*

• Define the QUANTIFICATION process */ process QUANTIFICATION { input: path salmon_index tuple val(sample_id), path(reads)

  output: path "$sample_id"

  script: """ tracer tool quant v2 salmon quant --threads ${task.cpus} --libType=U -i ${salmon_index} -1 ${reads[0]} -2 ${reads[1]} -o ${sample_id} tracer end """ }

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

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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.