Collapse FASTQ Files

Introduction

Inputs

This pipeline is general purpose for preparing FASTQ read files but was specifically developed to prepare data for RiboSeq.Org. Inputs for this pipeline may vary. Options include:

• Study accession
• Sample accession list
• Path to FASTQ directory

Outputs

Collapsed Read File

The primary output is a gzipped collapsed read file of the following format:

>read<read_number>_x<read_count>
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

where:

• <read_number> signifies that this is the nth read processed.
• <read_count> signifies how many times reads with this exact sequence was seen

FastQC Report

The html report for each sample is outputted

FastP

The html report from FastP

MultiQC Report

Combined report for each pipeline run. Merged FastP and FastQC

Requirements

This pipeline can be run using each of the following container methods

Method	Instructions
Singularity	docs.syslabs.io
Docker	docs.docker.com
Conda	docs.conda.io

Setup

Singularity

sudo singularity build singularity/pipeline Singularity

Then as the profile singularity specifies container = 'singularity/pipeline' use the following to execute:

nextflow run main.nf -profile singularity

Docker

docker build . -t pipeline-image

Then as the profile docker specifies container = 'pipeline-image:latest' use the following to execute:

nextflow run main.nf -profile docker

Conda

Create a conda definition yaml file eg. here

nextflow run main.nf -profile conda

Usage

Call the pipeline directly

nextflow run main.nf

Run with all the frills

bash scripts/run-w-frills <params-file> <profile name from nextflow.config>

Example

bash scripts/run-w-frills example_parameters.yml standard