Nextflow + Docker tutorial

This repository contains the tutorial material for the Parallel distributed computational workflows with Nextflow and Docker containers course.

Prerequisite

• Java 7 or 8
• Docker engine 1.10.x (or higher)

Installation

Install Nextflow by using the following command:

curl -fsSL get.nextflow.io | bash

The above snippet creates the nextflow launcher in the current directory. Complete the installation moving it into a directory on your PATH eg:

mv nextflow $HOME/bin

Finally, clone this repository with the following command:

git clone https://github.com/nextflow-io/crg-course-nov16.git && cd crg-course-nov16

Nextflow hands-on

During this tutorial you will implement a proof of concept of a RNA-Seq pipeline which:

1. Indexes a genome file.
2. Maps read pairs against the genome.
3. Performs quantification.

Step 1 - Command line parameters

The script rna-ex1.nf defines the pipeline input parameters. Run it by using the following command:

nextflow run rna-ex1.nf

Try to specify a different input parameter, for example:

nextflow run rna-ex1.nf --genome this/and/that

Step 2 - Build genome index

The second example adds the buildIndex process. It takes the genome file as input and creates the genome index by using the bowtie-build tool.

Try to run it by using the command:

nextflow run rna-ex2.nf

The execution will fail because Bowtie is not installed in the test environment.

Add the command line option -with-docker to launch the execution through a Docker container as shown below:

nextflow run rna-ex2.nf -with-docker

This time it works because it uses the Docker container nextflow/rnatoy:1.3 defined in the nextflow.config file.

In order to avoid to add the option -with-docker add the following line in the nextflow.config file:

docker.enabled = true

Step 3 - Collect read files by pairs

This step shows how to match read files into pairs, so thay can be mapped by TopHat.

Edit the script rna-ex3.nf and add the following statement as the last line:

read_pairs.println()

Save it and execute it with the following command:

nextflow run rna-ex3.nf

Try it again specifying different read files by using a glob pattern:

nextflow run rna-ex3.nf --reads 'data/ggal/reads/*_{1,2}.fq'

It shows how read files matching the pattern specified are grouped in pairs having the same prefix.

Step 4 - Map sequence reads

The script rna-ex4.nf adds the mapping process. Note how it declares three inputs: the genome fasta file, the genome index file produced by the buildIndex process and the read pairs. Also note as the last input is defined as a set ie. it's composed by different elements: the pair ID, the first read file and the second read file.

Execute it by using the following command:

nextflow run rna-ex4.nf -resume

The -resume option skips the execution of any step that has been processed in a previous execution.

Try to execute it with more read files as shown below:

nextflow run rna-ex4.nf -resume --reads 'data/ggal/reads/*_{1,2}.fq'

Step 5 - Perform reads quantification

This step adds the quantification step to the example script. It takes the annotation file and the bam files produced by TopHat and outputs the transcripts gtf files.

You can run it by using the following command:

nextflow run rna-ex5.nf -resume --reads 'data/ggal/reads/*_{1,2}.fq' 

Step 6 - Define the pipeline output

This step shows how produce the pipeline output to a folder of your choice by using the publishDir directive.

Run the example by using the following command:

nextflow run rna-ex6.nf -resume --reads 'data/ggal/reads/*_{1,2}.fq' 

Then you will find the quantification files in the folder results.

Modify the rna-ex6.nf script by adding the following line at the beginning of the file:

params.outdir = 'results'

Then, look for the publishDir directive in the makeTranscript process, and replace the 'results' string with the params.outdir parameter.

Finally run it again with the following command:

nextflow run rna-ex6.nf -resume --reads 'data/ggal/reads/*_{1,2}.fq' --outdir my_transcripts

You will find the transcripts produced by the pipeline in the my_transcripts folder.

Step 7 - Handle completion event

This step shows how to execute an action when the pipeline completes the execution.

Note that Nextflow processes define the execution of asynchronous tasks i.e. they are not executed one after another as they are written in the pipeline script as it would happen in a common iperative programming language.

The script uses the workflow.onComplete event handler to print a confirmation message when the script completes.

Try to run it by using the following command:

nextflow run rna-ex7.nf -resume --reads 'data/ggal/reads/*_{1,2}.fq'

Step 8 - Manage custom scripts

Real world pipelines use a lot of custom user scripts (BASH, R, Python, etc). Nextflow allows you to use and manage all these scripts in consistent manner. Simply put them in a directory named bin in the pipeline project root. They will be automatically added to the pipeline execution PATH.

For example, create a file named quantify.sh with the following content:

#!/bin/bash 
set -e 
set -u

annot=${1}
bam_file=${2}
pair_id=${3}

cufflinks --no-update-check -q -G $annot ${bam_file}
mv transcripts.gtf transcript_${pair_id}.gtf

Save it, grant the execute permission and move it under the bin directory as shown below:

chmod +x quantify.sh
mkdir -p bin 
mv quantify.sh bin

Then, open the rna-ex7.nf file and replace the makeTranscript process with the following code:

process makeTranscript {
    tag "$pair_id"
    publishDir params.outdir, mode: 'copy'  
       
    input:
    file annot from annotation_file 
    set pair_id, file(bam_file) from bam
     
    output:
    set pair_id, file('transcript_*.gtf') into transcripts
 
    """
    quantify.sh $annot $bam_file $pair_id
    """
}

For the sake of simplicity of this example, the cpus parameter it's ignored.

Run it as before:

nextflow run rna-ex7.nf -resume --reads 'data/ggal/reads/*_{1,2}.fq'

Step 9 - Publish to GitHub (bonus)

Here you will lean how to publish your pipeline on GitHub and share it with other people and allowing you to track all the project dependencies and changes with ease.

Setup your git credentials:

git config --config user.name "your name"
git config --config user.email your@email.com 

Create a new empty project folder that will contain the files you want to upload to GitHub eg.

mkdir $HOME/rnaseq-demo
cd $HOME/rnaseq-demo

Create a new project on GitHub to host your pipeline, and follow the instruction provided by it to publish the project in the project in the folder $HOME/rnaseq-demo/ in that repository.

Note: make sure to use the same email address you have defined in your git configuration setup with the previous commands.

Finally, copy the pipeline files and data and upload to the GitHub repository

cp $HOME/crg-course-nov16/rna-ex6.nf $HOME/rnaseq-demo/main.nf
cp $HOME/crg-course-nov16/nextflow.config $HOME/rnaseq-demo/
cp -r $HOME/crg-course-nov16/bin $HOME/rnaseq-demo/
cp -r $HOME/crg-course-nov16/data $HOME/rnaseq-demo/

git add bin/ data/ main.nf nextflow.config 
git commit -m 'Added pipeline files'
git push 

When done, you will be able to run your pipeline by using the following command:

nextflow run <your-github-user-name>/rnaseq-demo

Manage revisions (bonus)

Git and GitHub are tools specifically designed to track project changes and versions. You can use Git tags, branches or commit IDs to maintain an history revision of your pipeline projects.

Nextflow integrates these tools making possible to run any revision of your pipeline by simply specifying it on the run command line by using the -revision option, as shown below:

nextflow run <project name> -r <revision name>

The list of available revision can be list by using the following command:

nextflow info <project-name>

Docker hands-on

Get practice with basic Docker commands to pull, run and build your own containers.

A container is a ready-to-run Linux environment which can be executed in an isolated manner from the hosting system. It has own copy of the file system, processes space, memory management, etc.

Containers are a Linux feature known as Control Groups or Ccgroups introduced with kernel 2.6.

Docker adds to this concept an handy management tool to build, run and share container images.

These images can be uploaded and published in a centralised repository know as Docker Hub, or hosted by other parties like for example Quay.

Step 1 - Run a container

Run a container is easy as using the following command:

docker run <container-name> 

For example:

docker run hello-world  

Step 2 - Pull a container

The pull command allows you to download a Docker image without running it. For example:

docker pull debian:wheezy 

The above command download a Debian Linux image.

Step 3 - Run a container in interactive mode

Launching a BASH shell in the container allows you to operate in an interactive mode in the containerised operating system. For example:

docker run -it debian:wheezy bash 

Once launched the container you wil noticed that's running as root (!). Use the usual commands to navigate in the file system.

To exit from the container, stop the BASH session with the exit command.

Step 4 - Your first Dockerfile

Docker images are created by using a so called Dockerfile i.e. a simple text file containing a list of commands to be executed to assemble and configure the image with the software packages required.

In this step you will create a Docker image containing the Samtools and Bowtie2 tools.

In order to build a Docker image, start creating an empty directory eg. ~/docker-tutorial and change to it:

mkdir -p ~/docker-tutorial && cd ~/docker-tutorial 

Warning: the Docker build process automatically copies all files that are located in the current directory to the Docker daemon in order to create the image. This can take a lot of time when big/many files exist. For this reason it's important to always work in a directory containing only the files you really need to include in your Docker image. Alternatively you can use the .dockerignore file to select the path to exclude from the build.

Then use your favourite editor eg. vim to create a file named Dockerfile and copy the following content:

FROM debian:wheezy 

MAINTAINER <your name>

RUN apt-get update --fix-missing && \
  apt-get install -q -y python wget unzip samtools

When done save the file.

Step 5 - Build the image

Build the Docker image by using the following command:

docker build -t my-image .

Note: don't miss the dot in the above command. When it completes, verify that the image has been created listing all available images:

docker images

Step 6 - Add a software package to the image

Add the Bowtie package to the Docker image by adding to the Dockerfile the following snippet:

RUN wget --no-check-certificate -O bowtie.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.7/bowtie2-2.2.7-linux-x86_64.zip/download && \
  unzip bowtie.zip -d /opt/ && \
  ln -s /opt/bowtie2-2.2.7/ /opt/bowtie && \
  rm bowtie.zip 

ENV PATH $PATH:/opt/bowtie2-2.2.7/

Save the file and build again the image with the same command as before:

docker build -t my-image .

You will notice that it creates a new Docker image with the same name but with a different image ID.

Step 7 - Run Bowtie in the container

Check that everything is fine running Bowtie in the container as shown below:

docker run my-image bowtie2 --version

You can even launch a container in an interactive mode by using the following command:

docker run -it my-image bash

Step 8 - File system mounts

Create an genome index file by running Bowtie in the container.

Try to run Bowtie in the container with the following command:

docker run my-image \
  bowtie2-build ~/crg-course-nov16/data/ggal/genome.fa genome.index

The above command fails because Bowtie cannot access the input file.

This happens because the container runs in a complete separate file system and it cannot access the hosting file system by default.

You will need to use the --volume command line option to mount the input file(s) eg.

docker run --volume ~/crg-course-nov16/data/ggal/genome.fa:/genome.fa my-image \
  bowtie2-build /genome.fa genome.index

An easier way is to mount a parent directory to an identical one in the container, this allows you to use the same path when running it in the container eg.

docker run --volume $HOME:$HOME --workdir $PWD my-image \
  bowtie2-build ~/crg-course-nov16/data/ggal/genome.fa genome.index

Step 9 - Upload the container in the Docker Hub (bonus)

Publish your container in the Docker Hub to share it with other people.

Create an account in the https://hub.docker.com web site. Then from your shell terminal run the following command, entering the user name and password you specified registering in the Hub:

docker login 

Tag the image with your Docker user name account:

docker tag my-image <user-name>/my-image 

Finally push it to the Docker Hub:

docker push <user-name>/my-image 

After that anyone will be able to download it by using the command:

docker pull <user-name>/my-image 

Deploy a NF pipeline in the CRG cluster

Nextflow supports different execution platforms. This means that your script can be executed in a single computer, a cluster or a cloud by simply providing a configuration file that specify what computational platform you want to use.

For the sake of this tutorial you will run the RNA-Toy pipeline in the CRG cluster.

Log-in the CRG cluster by using the following cluster:

ssh <sitXX>@ant-login.linux.crg.es

• Replace the <sitXX> string with the user name that you have been assigned.

Create a project directory eg. rnatoy and create a file named nextflow.config with the following content:

process.executor = 'crg' 
process.queue = 'course'
process.scratch = true
process.time = '1h'
process.memory = '1G'
docker.enabled = true

Then launch the execution of the pipeline by using the following command:

nextflow run rnatoy

When completed you will find the pipeline output in the results folder.

Run the pipeline against a real dataset

Create a new folder to run the pipeline against the mouse genome dataset eg:

mkdir -p $HOME/mouse-run
cd $HOME/mouse-run

Then create the nextflow.config file with the following content:

params.reads = "/software/rg/rnaseq/data/*_{1,2}.fastq.gz"
params.annot = "/software/rg/rnaseq/refs/mm65.long.ok.sorted.gtf"
params.genome = "/users/cn/ptommaso/projects/nf-course/mouse_genome_mm9_chr1.fa" 

process.executor = 'crg' 
process.queue = 'course'
process.scratch = true
process.time = '1h'
process.memory = '8G'
process.cpus = 4 
process.$buildIndex.cpus = 8 

docker.enabled = true
trace.enabled = true

When done, launch the execution by using this command:

nextflow run rnatoy -bg > log

The -bg will launch NF in the background, to check the execution status you can follow the log as shown below:

tail -f log

Automatic errors fail over

When running large scale pipelines launching thousands of jobs on many different computing nodes errors are not a remote event.

Nextflow allows failing tasks to be automatically re-executed, in this way it's possible to address temporary failures such as failing hardware or network hiccups. In order to enable automatic jobs re-execution add the following setting in the nextflow.config file:

process.errorStrategy = 'retry'

A more common source of errors in computational pipeline are peaks in computing resources, allocated by a jobs exceeding the original resource request. In this context automatically re-executing the failed task is useless because it would simply replicate the same error condition.

A common solution consists of increasing the resource request for the needs of the most consuming job, even though this will result in a suboptimal allocation of most of the jobs that are less resource hungry.

Nextlow allows resources to be defined in a dynamic manner. In this way it is possible to increase the memory request when rescheduling a failing task execution. For example:

process.memory = { 1.GB * task.attempt }
process.errorStrategy { task.exitStatus == 140 ? 'retry' : 'terminate' }

By using the above settings pipeline a task will initially request one GB of memory. In case of an error it will be rescheduled requesting 2 GB and so on, until it is executed successfully or the limit of times a task can be retried is reached, forcing the termination of the pipeline.

Deploy a NF pipeline in the AWS cloud (bonus)

Nextflow pipelines can be seamlessly executed in the Amazon cloud. All you need is an AWS user account a base Amazon VM image (AMI) that will be used to setup the computing cluster in the cloud.

The following screen cast shows how to configure, setup the cluster and launch the pipeline execution in the AWS cloud in a few commands:

Assignment

Create a two steps pipeline that given any number of protein sequence FASTA files creates a phylogenetic tree for each or them. Bonus: use a Docker container to isolate and deploy the binary dependencies.

Tip

Use Clustalw2 to align the protein sequences. Example command line:

clustalw2 -infile=sample.fa -output=phylip -outfile=aln.phy

Use RAxML to create the phylogenetic tree. Example command line:

raxmlHPC -f d -j -p 9 -T 2 -m PROTGAMMALG -s aln.phy -n aln       

Use the input protein sequence FASTA files in the following folder:

$HOME/crg-course-nov16/data/prot

Possible implementation: https://github.com/nextflow-io/phytoy-nf