bio-workflow-management-nextflow-pipelines

Version Compatibility

Reference examples tested with: FastQC 0.12+, MultiQC 1.21+, Nextflow 23.10+, Salmon 1.10+, Snakemake 8.0+, fastp 0.23+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Nextflow Pipelines

"Create a scalable containerized pipeline with Nextflow" → Build DSL2 workflows with process definitions, channel-based data flow, Docker/Singularity container support, and cloud execution (AWS, Google Cloud) for portable bioinformatics analysis.

• CLI: nextflow run main.nf for pipeline execution
• Groovy: DSL2 process/workflow syntax for pipeline definition

Basic Pipeline Structure

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

params.reads = "data/*_{1,2}.fq.gz"
params.outdir = "results"

process FASTQC {
    input:
    tuple val(sample_id), path(reads)

    output:
    path("*.html"), emit: html
    path("*.zip"), emit: zip

    script:
    """
    fastqc ${reads}
    """
}

workflow {
    Channel.fromFilePairs(params.reads)
        | FASTQC
}

DSL2 Modules

// modules/fastqc.nf
process FASTQC {
    tag "${sample_id}"
    publishDir "${params.outdir}/qc", mode: 'copy'

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

    output:
    tuple val(sample_id), path("*.html"), emit: html
    tuple val(sample_id), path("*.zip"), emit: zip

    script:
    """
    fastqc -t ${task.cpus} ${reads}
    """
}

// main.nf
include { FASTQC } from './modules/fastqc'
include { ALIGN } from './modules/align'

workflow {
    reads_ch = Channel.fromFilePairs(params.reads)
    FASTQC(reads_ch)
    ALIGN(reads_ch)
}

Config File

// nextflow.config
params {
    reads = "data/*_{1,2}.fq.gz"
    outdir = "results"
    genome = "ref/genome.fa"
}

process {
    cpus = 4
    memory = '8 GB'
    time = '2h'

    withName: 'ALIGN' {
        cpus = 16
        memory = '32 GB'
    }
}

profiles {
    docker {
        docker.enabled = true
    }
    singularity {
        singularity.enabled = true
    }
    slurm {
        process.executor = 'slurm'
    }
}