Chapter 3: Processes, Directives & Script Blocks

Chapter 3: Processes, Directives & Script Blocks

A Process is the fundamental unit of execution in Nextflow. Each process runs in its own isolated temporary working directory (e.g. work/ab/c123.../), executing command-line scripts inside specified environments or containers.

1. Complete Anatomy of a Production Process

process FASTQC {
    tag "FastQC on ${sample_id}"
    label 'process_low'
    publishDir "results/fastqc", mode: 'copy', overwrite: true

    cpus 4
    memory '8 GB'
    time '2h'
    container 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'

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

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

    when:
    task.ext.when == null || task.ext.when

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

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        fastqc: \$(fastqc --version | sed -e "s/FastQC v//g")
    END_VERSIONS
    """
}

2. Critical Directives Explained

• publishDir: By default, Nextflow saves task outputs in isolated work/ scratch directories. publishDir creates symlinks or copies final deliverables into an organized results folder.
• tag: Displays clean human-readable identifiers in the Nextflow console terminal logs.
• emit:: Labels output channels with explicit names, enabling clean referencing in workflows (e.g. FASTQC.out.html).

3. Script vs. Shell Blocks (Bash Variable Escaping)

In standard script: blocks, Nextflow interpolates variables starting with $ as Nextflow variables. To reference an underlying Bash variable, you must escape it with a backslash (\${BASH_VAR}). Alternatively, use the shell: block with !{nextflow_var} syntax to preserve raw Bash syntax untouched.