ATACSeq Nextflow workflow

This workflow takes FASTQs, performs alignment, QC, and peak-calling for ATACSeq analysis. Additional annotation and analyses are found in ATACSeq_postpeakcalling_workflow.R.

Prerequisites

• bowtie2
• samtools
• bedtools
• deeptools
• MACS currently macs3 at the time of this workflow's completion
• picard optional if you prefer to use it instead of samtools for removing duplicate reads, uncomment in the appropriate line in main.nf

Preparation

1. Install bowtie2 index appropriate for your species after creating them from scratch or downloading from here
2. Similarly, install blacklist files appropriate for your species from here in a Databases_directory/
3. Create output_directory/ where you want outputs to go and edit samplesheet.csv to name your samples and point to your FASTQ files

After this you have two options:

OPTION A : Run with tools installed on your system:

4a. Install all tools above locally and verify that they are callable from the command prompt

5a. Edit the params.xxx section of main.nf to change tool parameters. Alternatively, you can pass parameters in when calling nextflow run in step 6a below

6a. Run the workflow:

nextflow run https://github.com/ptvan/ATACseq -r main --csv <samplesheet.csv> --output ~/<output_directory>

OPTION B: Run with dockerized tools:

4b. Pull the Docker image containing all the tools from: nulzilla/atacseq-dkr:

docker pull nulzilla/atacseq-dkr

5b. Start up Docker container with your FASTQ_directory/ and Databases_directory/ mounted:

docker run -it -v ./:/pipeline/nextflow:ro -v <FASTQ_directory>:/root/working/raw_data -v <Databases_directory/>:/root/working/Databases:ro <$DOCKER_IMAGE_ID> /bin/bash

6b. Run the workflow on mounted directories inside the Docker image:

nextflow run /pipeline/main.nf --csv --output ~/working/raw_data/output/