Nextflow: Pipeline Lift: RNASeq

How to lift a simple NextFlow pipeline?

In this tutorial, we will be using the example RNASeq pipeline nextflow.io to demonstrate the process of lifting a simple Nextflow pipeline over to ICA.

This approach is applicable in situations where your main.nf file contains all your pipeline logic and illustrates what the liftover process would look like.

Creating the pipeline

Select Projects > your_project > Flow > Pipelines. From the Pipelines view, click the Nextflow button to start creating a Nextflow pipeline.

In the Information tab, add values for the required Code (unique pipeline name) and Description fields. Nextflow Version and Storage size defaults to preassigned values.

How to modify the main.nf file

Copy and paste the RNASeq Nextflow pipeline into the main.nf tab. The following comparison highlights the differences between the original file and the version for deployment in ICA. The main difference is the explicit specification of containers and pods within processes. Additionally, some channels' specification are modified, and a debugging message is added. When copying and pasting, be sure to remove the text highlighted in red (marked with -) and add the text highlighted in green (marked with +).

#!/usr/bin/env nextflow

+nextflow.enable.dsl=2
 
/*
 * 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"
params.outdir = "results"

+println("All input parameters: ${params}")
 
workflow {
-    read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
+    read_pairs_ch = channel.fromFilePairs("${params.reads}/*_{1,2}.fq")
 
-    INDEX(params.transcriptome)
+    INDEX(Channel.fromPath(params.transcriptome))
     FASTQC(read_pairs_ch)
     QUANT(INDEX.out, read_pairs_ch)
}
 
process INDEX {
-    tag "$transcriptome.simpleName"
+    container 'quay.io/nextflow/rnaseq-nf:v1.1'
+    pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
 
    input:
    path transcriptome
 
    output:
    path 'index'
 
    script:
    """
    salmon index --threads $task.cpus -t $transcriptome -i index
    """
}
 
process FASTQC {
+    container 'quay.io/nextflow/rnaseq-nf:v1.1'
+    pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'

    tag "FASTQC on $sample_id"
    publishDir params.outdir
 
    input:
    tuple val(sample_id), path(reads)
 
    output:
    path "fastqc_${sample_id}_logs"
 
    script:
-    """
-    fastqc.sh "$sample_id" "$reads"
-    """
+    """
+    # we need to explicitly specify the output directory for fastqc tool
+    # we are creating one using sample_id variable
+    mkdir fastqc_${sample_id}_logs
+    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
+    """
}
 
process QUANT {
+    container 'quay.io/nextflow/rnaseq-nf:v1.1'
+    pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'

    tag "$pair_id"
    publishDir params.outdir
 
    input:
    path 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
    """
}

The XML configuration

In the XML configuration, the input files and settings are specified. For this particular pipeline, you need to specify the transcriptome and the reads directory. Navigate to the XML Configuration tab and paste the following:

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<pd:pipeline xmlns:pd="xsd://www.illumina.com/ica/cp/pipelinedefinition" code="" version="1.0">
    <pd:dataInputs>
        <pd:dataInput code="reads" format="UNKNOWN" type="DIRECTORY" required="true" multiValue="false">
            <pd:label>Folder with FASTQ files</pd:label>
            <pd:description></pd:description>
        </pd:dataInput>
        <pd:dataInput code="transcriptome" format="FASTA" type="FILE" required="true" multiValue="false">
            <pd:label>FASTA</pd:label>
            <pd:description>FASTA file</pd:description>
        </pd:dataInput>
    </pd:dataInputs>
    <pd:steps/>
</pd:pipeline>

Click the Generate button (at the bottom of the text editor) to preview the launch form fields.

Click the Save button to save the changes.

Running the pipeline

Go to the Pipelines page from the left navigation pane. Select the pipeline you just created and click Start New Analysis.

Fill in the required fields indicated by red "*" sign and click on Start Analysis button. You can monitor the run from the Analyses page. Once the Status changes to Succeeded, you can click on the run to access the results page.