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Update rnaseq example to new syntax #474

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Update rnaseq example
christopher-hakkaart Mar 23, 2026
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Tidy duplicated links
christopher-hakkaart Mar 23, 2026
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7 changes: 0 additions & 7 deletions src/components/Footer.astro
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Expand Up @@ -111,13 +111,6 @@ import LogoSeqera from "../../public/img/assets/Logo_Seqera_white.svg";
>Machine Learning pipeline</a
>
</li>
<li>
<a
class="text-white font-inter text-xs font-normal leading-normal"
href="https://github.com/nextflow-io/rnaseq-nf"
target="_blank">Simple RNAseq pipeline</a
>
</li>
<li>
<a
class="text-white font-inter text-xs font-normal leading-normal"
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6 changes: 0 additions & 6 deletions src/components/Menu/Menu.tsx
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Expand Up @@ -216,12 +216,6 @@ const Menu = ({}) => {
Machine Learning pipeline
</a>
</li>
<li>
<a href="https://github.com/nextflow-io/rnaseq-nf" target="_blank" tabIndex={0}>
Simple RNAseq pipeline
<img src="/img/assets/external-link-arrow.svg" alt="External link" className="externalLink inline-block" />
</a>
</li>
<li>
<a href="http://nextflow-io.github.io/patterns/index.html" target="_blank" tabIndex={0}>
Implementation patterns
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118 changes: 56 additions & 62 deletions src/pages/rna-seq-pipeline.md
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Expand Up @@ -7,95 +7,89 @@ layout: "@layouts/ExampleLayout.astro"
<h2>RNA-Seq pipeline</h2>

<p class="">
This example shows how to put together a basic RNA-Seq pipeline. It maps a collection of read-pairs to a given reference genome and outputs the respective transcript model.
This pipeline shows an example of a basic for RNA-Seq analysis that performs quality control, transcript quantification, and result aggregation. The pipeline processes paired-end FASTQ files, generates quality control reports with FastQC, quantifies transcripts with Salmon, and produces a unified report with MultiQC.
</p>

```groovy
#!/usr/bin/env nextflow

/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
// Parameter inputs
params.reads = "${baseDir}/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "${baseDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
params.multiqc = "${baseDir}/multiqc"


// Component imports
include { RNASEQ } from './modules/rnaseq'
include { MULTIQC } from './modules/multiqc'


// Workflow block
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )

INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
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()

process INDEX {
tag "$transcriptome.simpleName"
read_pairs_ch = channel.fromFilePairs(params.reads, checkIfExists: true, flat: true)

input:
path transcriptome
(fastqc_ch, quant_ch) = RNASEQ(read_pairs_ch, params.transcriptome)

output:
path 'index'
multiqc_files_ch = fastqc_ch.mix(quant_ch).collect()

script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
MULTIQC(multiqc_files_ch, params.multiqc)

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

process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
</div>

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

output:
path "fastqc_${sample_id}_logs"
The pipeline uses two imported components:

script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
<p style="padding-left: 40px;">&#8226; <code>RNASEQ</code>: a subworkflow that contains three processes:</p>

process QUANT {
tag "$pair_id"
publishDir params.outdir
<p style="padding-left: 80px;">&#8226; <code>INDEX</code>: creates a Salmon index from the transcriptome (runs once)</p>

input:
path index
tuple val(pair_id), path(reads)
<p style="padding-left: 80px;">&#8226; <code>FASTQC</code>: analyzes each sample in parallel</p>

output:
path pair_id
<p style="padding-left: 80px;">&#8226; <code>QUANT</code>: quantifies transcripts for each sample after indexing completes</p>

script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
```
<p style="padding-left: 40px;">&#8226; <code>MULTIQC</code>: aggregates all quality control and quantification outputs into a comprehensive HTML report</p>

</div>
The `workflow` block uses `channel.fromFilePairs` to create a channel of paired-end read files. It passes the reads and transcriptome to the `RNASEQ` subworkflow, then mixes the FastQC and quantification outputs and passes them to `MULTIQC`.

<br>

### Try it in your computer
### Get started

To run this pipeline on your computer, you will need:
To run this pipeline:

- Unix-like operating system
- Java 17 (or higher)
- Docker
<p style="padding-left: 40px;">1. <a href="https://docs.seqera.io/nextflow/install">Install Nextflow</a> (version 25.10 or later)</p>

Install Nextflow by entering the following command in the terminal:
<p style="padding-left: 40px;">2. <a href="https://docs.docker.com/get-started/get-docker/"> Install Docker</a></p>

$ curl -fsSL get.nextflow.io | bash
<p style="padding-left: 40px;">3. Run the pipeline directly from its GitHub repository:</p>

Then launch the pipeline with this command:
<div style="padding-left: 60px; margin-top: 1rem;">

$ nextflow run rnaseq-nf -with-docker
```
nextflow run nextflow-io/rnaseq-nf -profile docker
```

</div>

It will automatically download the pipeline [GitHub repository](https://github.com/nextflow-io/rnaseq-nf) and the associated Docker images, thus the first execution may take a few minutes to complete depending on your network connection.
<br>

**NOTE**: To run this example with versions of Nextflow older than 22.04.0, you must include the `-dsl2` flag with `nextflow run`.
See the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) GitHub repository for all of the pipeline code and the [rnaseq-nf tutorial](https://nextflow.io/docs/stable/tutorials/rnaseq-nf.html) for a full pipeline description.
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