Simple RNA-Seq pipeline

Last updated on 2024-12-04 | Edit this page

Estimated time: 60 minutes

Overview

Questions

How can I create a Nextflow pipeline from a series of unix commands and input data?
How do I log my pipelines parameters?
How can I manage my pipeline software requirements?
How do I know when my pipeline has finished?
How do I see how much resources my pipeline has used?

Objectives

Create a simple RNA-Seq pipeline.
Use the log.info function to print all the pipeline parameters.
Print a confirmation message when the pipeline completes.
Use a conda environment.yml file to install the pipeline’s software requirement.
Produce an execution report and generate run metrics from a pipeline run.

We’re now set to develop a multi-step pipeline using Nextflow, for analyzing and performing quality control on our yeast RNA-Seq experiment.

In this RNA-Seq pipeline, we’ll undertake the following steps to thoroughly analyze gene expression data:

Quality Control with FastQC: FastQC assesses the quality of the data by generating reports that highlight any potential issues, such as low-quality sequences or contamination. FastQC’s output includes an HTML report and a directory containing detailed analyses, which are essential for evaluating the integrity of the sequencing data.

BASH

$ mkdir fastqc_<sample_id>_logs
$ fastqc -o fastqc_<sample_id>_logs -f fastq -q <reads>

Transcriptome Indexing with Salmon: Salmon is a tool to quantify transcript expression in RNA-seq data. The first step in the process is for Salmon to create an index of the transcriptome. This step involves processing a reference transcriptome, which allows for efficient and accurate mapping and quantification of RNA-Seq reads.

BASH

$ salmon index --threads <cpus> -t <transcriptome file> -i index

Quantification with Salmon: After indexing, Salmon is used for the quantification step. In this step, Salmon maps the reads to the transcriptome index and quantifies the transcript abundances. This process is crucial for determining the expression levels of genes in the sample.

BASH

$ salmon quant --threads <cpus> --libType=U -i <index> -1 <read1> -2 <read2> -o <pair_id>

Aggregating Reports with MultiQC: Finally, the pipeline employs MultiQC to aggregate logs and outputs from the FastQC and Salmon. MultiQC scans the outputs and compiles a summary report, which provides an overview of the results and highlights any areas that may need further investigation.

BASH

$ multiqc .

This pipeline provides an overview of RNA-Seq data, from quality control to expression quantification, culminating in an aggregated report for easy interpretation of the results.

To start move the episode’s nextflow scripts in the scripts/rnaseq_pipeline folder to your home directory.

BASH

$ cp scripts/rnaseq_pipeline/* .

This folder contains files we will be modifying in this episode.

Define the pipeline parameters

The first thing we want to do when writing a pipeline is define the pipeline parameters. The script script1.nf defines the pipeline input parameters.

GROOVY

//script1.nf
params.reads = "data/yeast/reads/*_{1,2}.fq.gz"
params.transcriptome = "data/yeast/transcriptome/*.fa.gz"


println "reads: $params.reads"

Run it by using the following command:

BASH

$ nextflow run script1.nf

We can specify a different input parameter using the --<params> option, for example :

GROOVY

$ nextflow run script1.nf --reads "data/yeast/reads/ref1*_{1,2}.fq.gz"

OUTPUT

reads: data/yeast/reads/ref1*_{1,2}.fq.gz

Add a parameter

Modify the script1.nf adding a third parameter named outdir and set it to results. This parameter will be used as the pipeline output directory.

Show me the solution

GROOVY

params.outdir = "results"

It can be useful to print the pipeline parameters to the screen. This can be done using the the log.info command and a multiline string statement. The string method .stripIndent() command is used to remove the indentation on multi-line strings. log.info also saves the output to the log execution file .nextflow.log.

GROOVY

log.info """\
         transcriptome: ${params.transcriptome}
         """
         .stripIndent()

log.info

Modify the script1.nf to print all the pipeline parameters by using a single log.info command and a multiline string statement. See an example here.

BASH

$ nextflow run script1.nf

Look at the output log .nextflow.log.

Show me the solution

Below is an example log.info command printing all the pipeline parameters.

GROOVY

log.info """\
        R N A S E Q - N F   P I P E L I N E    
        ===================================
        transcriptome: ${params.transcriptome}
        reads        : ${params.reads}
        outdir       : ${params.outdir}
        """
        .stripIndent()

BASH

$ less .nextflow.log

Recap

In this step you have learned:

How to define parameters in your pipeline script.
How to pass parameters by using the command line.
The use of $var and ${var} variable placeholders.
How to use multiline strings.
How to use log.info to print information and save it in the log execution file.

Create a transcriptome index file

Nextflow allows the execution of any command or user script by using a process definition.

For example,

BASH

$ salmon index --threads $task.cpus -t $transcriptome -i index

A process is defined by providing three main declarations:

The process inputs,
The process outputs
Finally the command script.

The second example, script2.nf adds,

The process INDEX which generate a directory with the index of the transcriptome. This process takes one input, a transcriptome file, and emits one output a salmon index directory.
A queue Channel transcriptome_ch taking the transcriptome file defined in params variable params.transcriptome.
Finally the script adds a workflow definition block which calls the INDEX process.

GROOVY

//script2.nf


/*
 * pipeline input parameters
 */
params.reads = "data/yeast/reads/*_{1,2}.fq.gz"
params.transcriptome = "data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"
params.outdir = "results"

println """\
         R N A S E Q - N F   P I P E L I N E
         ===================================
         transcriptome: ${params.transcriptome}
         reads        : ${params.reads}
         outdir       : ${params.outdir}
         """
         .stripIndent()


/*
 * define the `INDEX` process that create a binary index
 * given the transcriptome file
 */
process INDEX {

    input:
    path transcriptome

    output:
    path 'index'

    script:
    """
    salmon index --threads $task.cpus -t $transcriptome -i index
    """
}

transcriptome_ch = channel.fromPath(params.transcriptome)

workflow {
   INDEX()
}

Try to run it by using the command:

BASH

$ nextflow run script2.nf

OUTPUT

N E X T F L O W  ~  version 22.04.0
Launching `script2.nf` [happy_brown] DSL2 - revision: 90e932bb8d
R N A S E Q - N F   P I P E L I N E
===================================
transcriptome: data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz
reads        : data/yeast/reads/*_{1,2}.fq.gz
outdir       : results

Process `INDEX` declares 1 input channel but 0 were specified

 -- Check script 'script2.nf' at line: 41 or see '.nextflow.log' file for more details

The execution will fail because the program the process, INDEX , has not been passed any input channel.

Add the transcriptome_ch channel to the INDEX process call.

GROOVY

[truncated]
workflow {
   INDEX(transcriptome_ch)
}

Now try to run it again by using the command:

BASH

$ nextflow run script2.nf

Now the workflow will run successfully.

OUTPUT

N E X T F L O W  ~  version 22.04.0
Launching `script2.nf` [mad_aryabhata] DSL2 - revision: 811396b67b
R N A S E Q - N F   P I P E L I N E
===================================
transcriptome:data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz
reads        : data/yeast/reads/*_{1,2}.fq.gz
outdir       : results

executor >  local (1)
[c0/418d78] process > INDEX (1) [100%] 1 of 1 ✔

The INDEX process also defines one output channel. This channel will be populated with index directory created during process. To view the contents of the channel we can use the view operator.

View the contents of the index_ch

Assign the output of the INDEX process to the variable index_ch.
View the contents of the index_ch channel by using the view operator.

Show me the solution

GROOVY

[..truncated..]
workflow {
  index_ch=INDEX(transcriptome_ch)
  index_ch.view()
}

Recap

In this step you have learned:

How to define a process executing a custom command
How process inputs are declared
How to assign a channel as input to a process call
How process outputs are declared
How to print the content of a channel view()

Collect read files by pairs

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

The script script3.nf adds a line to create a channel, read_pairs_ch, containing fastq read pair files using the fromFilePairs channel factory.

GROOVY

//script3.nf
nextflow.enable.dsl = 2

/*
 * pipeline input parameters
 */
params.reads = "data/yeast/reads/ref1_{1,2}.fq.gz"
params.transcriptome = "data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"
params.outdir = "results"

log.info """\
         R N A S E Q - N F   P I P E L I N E
         ===================================
         transcriptome: ${params.transcriptome}
         reads        : ${params.reads}
         outdir       : ${params.outdir}
         """
         .stripIndent()


read_pairs_ch = Channel.fromFilePairs( params.reads )

We can view the contents of the read_pairs_ch by adding the following statement as the last line:

GROOVY

read_pairs_ch.view()

Now if we execute it with the following command:

BASH

$ nextflow run script3.nf

It will print an output similar to the one shown below that shows how the read_pairs_ch channel emits a tuple. The tuple is composed of two elements, where the first is the pattern matched by the glob pattern data/yeast/reads/ref1_{1,2}.fq.g, defined by the variable params.reads , and the second is a list representing the actual files.

OUTPUT

[..truncated..]
[ref1, [data/yeast/reads/ref1_1.fq.gz,data/yeast/reads/ref1_2.fq.gz]]

To read in other read pairs we can specify a different glob pattern in the params.reads variable by using --reads options on the command line. For example, the following command would read in add the ref samples:

BASH

$ nextflow run script3.nf --reads 'data/yeast/reads/ref*_{1,2}.fq.gz'

OUTPUT

[..truncated..]
[ref2, [data/yeast/reads/ref2_1.fq.gz, data/yeast/reads/ref2_2.fq.gz]]
[ref3, [data/yeast/reads/ref3_1.fq.gz, data/yeast/reads/ref3_2.fq.gz]]
[ref1, [data/yeast/reads/ref1_1.fq.gz, data/yeast/reads/ref1_2.fq.gz]]

Note File paths including one or more wildcards ie. *, ?, etc. MUST be wrapped in single-quoted characters to avoid Bash expanding the glob pattern on the command line.

We can also add a argument, checkIfExists: true , to the fromFilePairs channel factory to return an message if the file doesn’t exist.

GROOVY

//script3.nf
[..truncated..]
read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists: true )

If we now run the script with the --reads parameter data/yeast/reads/*_1,2}.fq.gz

BASH

$ nextflow run script3.nf --reads 'data/yeast/reads/*_1,2}.fq.gz'

it will return the message .

OUTPUT

[..truncated..]
No such file: data/yeast/reads/*_1,2}.fq.gz

Read in all read pairs

Add the checkIfExists: true argument to the fromFilePairs channel factory in script3.nf.
Using the command line parameter --reads, add a glob pattern to read in all the read pairs files from the data/yeast/reads directory.

Show me the solution

GROOVY

read_pairs_ch =Channel.fromFilePairs(params.reads, checkIfExists: true)

BASH

nextflow run script3.nf --reads 'data/yeast/reads/*_{1,2}.fq.gz'

OUTPUT

[..truncated..]
[temp33_1, [data/yeast/reads/temp33_1_1.fq.gz, data/yeast/reads/temp33_1_2.fq.gz]]
[ref2, [data/yeast/reads/ref2_1.fq.gz, data/yeast/reads/ref2_2.fq.gz]]
[temp33_3, [data/yeast/reads/temp33_3_1.fq.gz, data/yeast/reads/temp33_3_2.fq.gz]]
[ref3, [data/yeast/reads/ref3_1.fq.gz, data/yeast/reads/ref3_2.fq.gz]]
[temp33_2, [data/yeast/reads/temp33_2_1.fq.gz,data/yeast/reads/temp33_2_2.fq.gz]]
[etoh60_2, [data/yeast/reads/etoh60_2_1.fq.gz,data/yeast/reads/etoh60_2_2.fq.gz]]
[ref1, [data/yeast/reads/ref1_1.fq.gz, data/yeast/reads/ref1_2.fq.gz]]
[etoh60_3, [data/yeast/reads/etoh60_3_1.fq.gz, data/yeast/reads/etoh60_3_2.fq.gz]]
[etoh60_1, [data/yeast/reads/etoh60_1_1.fq.gz, data/yeast/reads/etoh60_1_2.fq.gz]]

Recap

In this step you have learned:

How to use fromFilePairs to handle read pair files
How to use the checkIfExists option to check input file existence

Perform expression quantification

The script script4.nf;

Adds the quantification process, QUANT.
Calls the QUANT process in the workflow block.

GROOVY

//script4.nf
..truncated..
/*
 * Run Salmon to perform the quantification of expression using
 * the index and the matched read files
 */
process QUANT {

    input:
    each index
    tuple val(pair_id), path(reads)

    output:
    path(pair_id)

    script:
    """
    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
    """
}
..truncated..
workflow {
  read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true )
  transcriptome_ch = Channel.fromPath( params.transcriptome, checkIfExists:true )

  index_ch=INDEX(transcriptome_ch)
  quant_ch=QUANT(index_ch,read_pairs_ch)
}

The index_ch channel, declared as output in the INDEX process, is used as the first input argument to the QUANT process.

The second input argument of the QUANT process, the read_pairs_ch channel, is a tuple composed of two elements: the pair_id and the reads.

Execute it by using the following command:

BASH

$ nextflow run script4.nf

You will see the execution of the index and quantification process.

Re run the command using the -resume option

BASH

$ nextflow run script4.nf -resume

The -resume option cause the execution of any step that has been already processed to be skipped.

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

BASH

$ nextflow run script4.nf -resume --reads 'data/yeast/reads/ref*_{1,2}.fq.gz'

OUTPUT

N E X T F L O W  ~  version 21.04.0
Launching `script4.nf` [shrivelled_brenner] - revision: c21df6839e
R N A S E Q - N F   P I P E L I N E
===================================
transcriptome: data/yeast/transcriptome/Saccharomyces_c
erevisiae.R64-1-1.cdna.all.fa.gz

reads        : data/yeast/reads/ref*_{1,2}.fq.gz
outdir       : results

executor >  local (8)
[02/3742cf] process > INDEX     [100%] 1 of 1, cached: 1 ✔
[9a/be3483] process > QUANT (9) [100%] 3 of 3, cached: 1 ✔

You will notice that the INDEX step and one of the QUANT steps has been cached, and the quantification process is executed more than one time.

When your input channel contains multiple data items Nextflow, where possible, parallelises the execution of your pipeline.

In these situations it is useful to add a tag directive to add some descriptive text to instance of the process being run.

Add a tag directive

Add a tag directive to the QUANT process of script4.nf to provide a more readable execution log.

Show me the solution

GROOVY

tag "quantification on $pair_id"

Data produced by the workflow during a process will be saved in the working directory, by default a directory named work. The working directory should be considered a temporary storage space and any data you wish to save at the end of the workflow should be specified in the process output with the final storage location defined in the publishDir directive.

Note: by default the publishDir directive creates a symbolic link to the files in the working this behaviour can be changed using the mode parameter.

Add a publishDir directive

Add a publishDir directive to the quantification process of script4.nf to store the process results into folder specified by the params.outdir Nextflow variable. Include the publishDir mode option to copy the output.

Challenge

Show me the solution

GROOVY

publishDir "${params.outdir}/quant", mode:'copy'

Recap

In this step you have learned:

How to connect two processes by using the channel declarations.
How to resume the script execution skipping already already computed steps.
How to use the tag directive to provide a more readable execution output.
How to use the publishDir to store a process results in a path of your choice.

Quality control

This step implements a quality control step for your input reads. The input to the FASTQC process is the same read_pairs_ch that is provided as input to the quantification process QUANT .

GROOVY

//script5.nf
[..truncated..]

/*
 * Run fastQC to check quality of reads files
 */
process FASTQC {
    tag "FASTQC on $sample_id"
    cpus 1

    input:
    tuple val(sample_id), path(reads)

    output:
    path("fastqc_${sample_id}_logs")

    script:
    """
    mkdir fastqc_${sample_id}_logs
    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads} -t ${task.cpus}
    """
}

[..truncated..]

workflow {
  read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true )
  transcriptome_ch = Channel.fromPath( params.transcriptome, checkIfExists:true )

  index_ch=INDEX(transcriptome_ch)
  quant_ch=QUANT(index_ch,read_pairs_ch)
}

Run the script script5.nf by using the following command:

BASH

$ nextflow run script5.nf -resume

The FASTQC process will not run as the process has not been declared in the workflow scope.

Add FASTQC process

Add the FASTQC process to the workflow scope of script5.nf adding the read_pairs_ch channel as an input. Run the nextflow script using the -resume option.

BASH

$ nextflow run script5.nf -resume

Show me the solution

GROOVY

workflow {
read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true )
transcriptome_ch = Channel.fromPath( params.transcriptome, checkIfExists:true )

index_ch = INDEX( transcriptome_ch )
quant_ch=QUANT(index_ch,read_pairs_ch)
fastqc_ch=FASTQC(read_pairs_ch)

}

Recap

In this step you have learned:

How to use the add a process to the workflow scope.
Add a channel as input to a process.

MultiQC report

This step collect the outputs from the quantification and fastqc steps to create a final report by using the MultiQC tool.

The input for the MULTIQC process requires all data in a single channel element. Therefore, we will need to combine the FASTQC and QUANT outputs using:

The combining operator mix : combines the items in the two channels into a single channel

GROOVY

//example of the mix operator
ch1 = Channel.of(1,2)
ch2 = Channel.of('a')
ch1.mix(ch2).view()

OUTPUT

1
2
a

The transformation operator collect collects all the items in the new combined channel into a single item.

GROOVY

//example of the collect operator
ch1 = Channel.of(1,2,3)
ch1.collect().view()

OUTPUT

[1, 2, 3]

Combining operators

Which is the correct way to combined mix and collect operators so that you have a single channel with one List item?

quant_ch.mix(fastqc_ch).collect()
quant_ch.collect(fastqc_ch).mix()
fastqc_ch.mix(quant_ch).collect()
fastqc_ch.collect(quant_ch).mix()

Show me the solution

You need to use the mix operator first to combine the channels followed by the collect operator to collect all the items in a single item.

In script6.nf we use the statement quant_ch.mix(fastqc_ch).collect() to combine and collect the outputs of the QUANT and FASTQC process to create the required input for the MULTIQC process.

GROOVY

[..truncated..]
//script6.nf
/*
 * Create a report using multiQC for the quantification
 * and fastqc processes
 */
process MULTIQC {
    publishDir "${params.outdir}/multiqc", mode:'copy'

    input:
    path('*')

    output:
    path('multiqc_report.html')

    script:
    """
    multiqc .
    """
}


workflow {
  read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true )
  transcriptome_ch = Channel.fromPath( params.transcriptome, checkIfExists:true )

  index_ch=INDEX(transcriptome_ch)
  quant_ch=QUANT(index_ch,read_pairs_ch)
  fastqc_ch=FASTQC(read_pairs_ch)
  MULTIQC(quant_ch.mix(fastqc_ch).collect())
}

Execute the script with the following command:

BASH

$ nextflow run script6.nf --reads 'data/yeast/reads/*_{1,2}.fq.gz' -resume

OUTPUT

N E X T F L O W  ~  version 21.04.0
Launching `script6.nf` [small_franklin] - revision: 9062818659
R N A S E Q - N F   P I P E L I N E
===================================
transcriptome: data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz
reads        : data/yeast/reads/*_{1,2}.fq.gz
outdir       : results

executor >  local (9)
[02/3742cf] process > INDEX                              [100%] 1 of 1, cached: 1 ✔
[9a/be3483] process > QUANT (quantification on etoh60_1) [100%] 9 of 9, cached: 9 ✔
[1f/b7b30a] process > FASTQC (FASTQC on etoh60_1)        [100%] 9 of 9, cached: 1 ✔
[2c/206fef] process > MULTIQC                            [100%] 1 of 1 ✔

It creates the final report in the results folder in the ${params.outdir}/multiqc directory.

Recap

In this step you have learned:

How to collect many outputs to a single input with the collect operator
How to mix two channels in a single channel using the mix operator.
How to chain two or more operators togethers using the . operator.

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 imperative programming language.

The script script7..nf uses the workflow.onComplete event handler to print a confirmation message when the script completes.

GROOVY

workflow.onComplete {
	log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc/multiqc_report.html\n" : "Oops .. something went wrong" )
}

This code uses the ternary operator that is a shortcut expression that is equivalent to an if/else branch assigning some value to a variable.

If expression is true? "set value to a" : "else set value to b"

Try to run it by using the following command:

BASH

$ nextflow run script7.nf -resume --reads 'data/yeast/reads/*_{1,2}.fq.gz'

OUTPUT

[..truncated..]
Done! Open the following report in your browser --> results/multiqc/multiqc_report.html

Metrics and reports

Nextflow is able to produce multiple reports and charts providing several runtime metrics and execution information.

The -with-report option enables the creation of the workflow execution report.
The -with-trace option enables the create of a tab separated file containing runtime information for each executed task, including: submission time, start time, completion time, cpu and memory used..
The -with-timeline option enables the creation of the workflow timeline report showing how processes where executed along time. This may be useful to identify most time consuming tasks and bottlenecks. See an example at this link.
The -with-dag option enables to rendering of the workflow execution direct acyclic graph representation. Note: this feature requires the installation of Graphviz, an open source graph visualization software, in your system.

More information can be found here.

Metrics and reports

Run the script7.nf with the reporting options as shown below:

BASH

$ nextflow run script7.nf -resume -with-report -with-trace -with-timeline -with-dag dag.png

Open the file report.html with a browser to see the report created with the above command.
Check the content of the file trace.txt or view timeline.html to find the longest running process.
View the dag.png

Show me the solution

The INDEX process should be the longest running process. dag.png The vertices in the graph represent the pipeline’s processes and operators, while the edges represent the data connections (i.e. channels) between them.

short running tasks

Note: runtime metrics may be incomplete for run short running tasks..

Key Points

Nextflow can combined tasks (processes) and manage data flows using channels into a single pipeline/workflow.
A Workflow can be parameterise using params . These value of the parameters can be captured in a log file using log.info
Nextflow can handle a workflow’s software requirements using several technologies including the conda package and enviroment manager.
Workflow steps are connected via their inputs and outputs using Channels.
Intermediate pipeline results can be transformed using Channel operators such as combine.
Nextflow can execute an action when the pipeline completes the execution using the workflow.onComplete event handler to print a confirmation message.
Nextflow is able to produce multiple reports and charts providing several runtime metrics and execution information using the command line options -with-report, -with-trace, -with-timeline and produce a graph using -with-dag.