Making reproducible workflows with

22-Oct-2025

Nextflow features

  • Generalisable
  • Portable
  • Scalable
  • Platform-agnostic
  • Based on Groovy and Java
  • Large active community in e.g. nf-core

Nextflow adoption

Nextflow has grown rapidly since its creation, and is the most commonly used workflow manager in bioinformatics since 2024. 1

Concepts and nomenclature

  • Channels contain data, e.g. input files
  • Processes run some kind of code, e.g. a script or a program
  • Tasks are instances of a process, one per process input
  • Each task is run in its own, isolated sub-directory

Anatomy of a process

process GET_SRA_BY_ACCESSION {

    input:
    val(sample)

    output:
    path("${sample}.fastq.gz")

    script:
    """
    fastq-dump ${sample} > ${sample}.fastq.gz
    """
}

Anatomy of a process

process GET_SRA_BY_ACCESSION {

    input:
    val(sample)

    output:
    tuple val(sample), path("${sample}.fastq.gz")

    script:
    """
    fastq-dump ${sample} > ${sample}.fastq.gz
    """
}

Anatomy of a process

process GET_SRA_BY_ACCESSION {

    cpus 2
    memory '8 GB'

    input:
    val(sample)

    output:
    tuple val(sample), path("${sample}.fastq.gz")

    script:
    """
    fastq-dump ${sample} > ${sample}.fastq.gz
    """
}

Anatomy of a process

process GET_SRA_BY_ACCESSION {

    cpus 2
    memory '8 GB'

    conda 'sra-tools=2.11.0'
    container 'ncbi/sra-tools:2.11.0'

    input:
    val(sample)

    output:
    tuple val(sample), path("${sample}.fastq.gz")

    script:
    """
    fastq-dump ${sample} > ${sample}.fastq.gz
    """
}

Anatomy of a workflow

workflow {

    // Define SRA input data channel
    ch_sra_ids = Channel.fromList ( ["SRR935090", "SRR935091", "SRR935092"] )

    // Define the workflow
    GET_SRA_BY_ACCESSION (
        ch_sra_ids
    )
}

Anatomy of a workflow

workflow {

    // Define SRA input data channel
    ch_sra_ids = Channel.fromList ( ["SRR935090", "SRR935091", "SRR935092"] )

    // Define the workflow
    GET_SRA_BY_ACCESSION (
        ch_sra_ids
    )
    RUN_FASTQC (
        GET_SRA_BY_ACCESSION.out
    )
}

Anatomy of a workflow

workflow {

    // Define SRA input data channel
    ch_sra_ids = Channel.fromList ( ["SRR935090", "SRR935091", "SRR935092"] )

    // Define the workflow
    GET_SRA_BY_ACCESSION (
        ch_sra_ids
    )
    RUN_FASTQC (
        GET_SRA_BY_ACCESSION.out
    )
    RUN_MULTIQC (
        RUN_FASTQC.out.collect()
    )
}

Executing Nextflow

Execute a workflow

$ nextflow run main.nf


Re-run using cached results

$ nextflow run main.nf -resume


Execute with a specific configuration file

$ nextflow run main.nf -c nextflow.config


Supply a custom parameter

$ nextflow run main.nf --param "value"


Use a pre-defined configuration profile

$ nextflow run main.nf -profile uppmax


Use Docker or Apptainer

$ nextflow run main.nf -with-docker
$ nextflow run main.nf -with-apptainer


Snakemake and Nextflow differences



Snakemake Nextflow
Language Python Groovy
Data Everything is a file Can use both files and values
Execution Working directory Each job in its own directory
Philosophy “Pull” “Push”
Dry-runs Yes No


  • Question: But, which one is the best?
  • Answer: Both - it’s mostly up to personal preference!

Questions?