Genomic Data Analysis II

Nextflow

Introduction

There will be no exercise for you to complete in nextflow this week. Instead, I have designed a simple nextflow script that can perform both single-end and paired-end analysis with kallisto by using if/else statements.

Furthermore, the script is capable of downloading the reference cDNA index file and performing kallisto index if neither file is not provided.

Single end data

Before we walk thorugh the script, you need to know how to handle single-end fastq files with nextflow. In the example below, we specify the paths to the fastq files using fromPath(). This will return a channel with the paths to the fastq files.

Save the below script and run it:

#!/usr/bin/env nextflow

params.input = "/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/*.fastq.gz"

Channel
      .fromPath(params.input)
      .set{ch_reads}

ch_reads.view()

/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/ctrl_2.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/ctrl_1.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/ctrl_3.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A375_1.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A375_2.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A375_3.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A549_1.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A549_2.fastq.gz
/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A549_3.fastq.gz

The channel outputs file paths. We want it to mimick fromFilePairs() and create a tuple with a key for each file path, so we can name the output directories when running kallisto quant for single end data.

Save the below script and run it:

#!/usr/bin/env nextflow

params.input = "/data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/*.fastq.gz"

Channel
      .fromPath(params.input)
      .map{ file -> [file.simpleName, file]}
      .set{ch_reads}

ch_reads.view()

[ctrl_2, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/ctrl_2.fastq.gz]
[ctrl_1, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/ctrl_1.fastq.gz]
[ctrl_3, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/ctrl_3.fastq.gz]
[A375_1, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A375_1.fastq.gz]
[A375_2, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A375_2.fastq.gz]
[A375_3, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A375_3.fastq.gz]
[A549_1, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A549_1.fastq.gz]
[A549_2, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A549_2.fastq.gz]
[A549_3, /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/A549_3.fastq.gz]

Now we can use the format tuple val(base), file(reads) from ch_reads for kallisto alignment.

Read here for descriptions on how to get unique IDs based on filenames using simpleName and baseName.

Nextflow script

Go to the main nextflow script available at this link: https://github.com/BarryDigby/barrydigby.github.io/blob/master/RNA-Seq/main.nf.

Save the contents as main.nf and invoke the help message by running nextflow run main.nf --help.

Note: the fastq files for the practical are located at: /data/MA5112/Practicals/RNA-Seq/Kallisto_Practical/Data/