Basic pipeline

This pipeline shows how to write a pipeline with two simple Bash processes. The first process splits a string into chunks, and the second process converts the lowercase letters in each chunk to uppercase. It also shows how to publish pipeline outputs to named directories.

// Default parameter input
params.str = "Hello world!"

// split process
process split {
    input:
    val x

    output:
    path 'chunk_*'

    script:
    """
    printf '${x}' | split -b 6 - chunk_
    """
}

// convert_to_upper process
process convert_to_upper {
    tag "$y"

    input:
    path y

    output:
    path 'upper_*'

    script:
    """
    cat $y | tr '[a-z]' '[A-Z]' > upper_${y}
    """
}

// Workflow block
workflow {
    main:
    ch_str = channel.of(params.str)
    ch_chunks = split(ch_str)
    ch_upper = convert_to_upper(ch_chunks.flatten())

    publish:
    lower = ch_chunks.flatten()
    upper = ch_upper
}

output {
    lower {
        path 'lower'
    }
    upper {
        path 'upper'
    }
}

Synopsis

This pipeline defines two processes:

• split: takes a string as input, splits it into 6-byte chunks, and writes the chunks to files with the prefix chunk_

• convert_to_upper: takes files as input, transforms their contents to uppercase letters, and writes the uppercase strings to files with the prefix upper_

The split output is emitted as a single element containing all chunk files. The flatten operator splits this combined element so that each file is treated as a sole element and processed independently by convert_to_upper.

The workflow block is organized into two sections:

• main: defines the workflow logic and how processes are connected via channels

• publish: declares which channels should be published as workflow outputs

The output block (outside the workflow) defines where and how each output should be published. In this example, the outputs from both processes are published in subdirectories (lower and upper) in the default results output directory (params.outdir).

To run this pipeline:

1. Install Nextflow (version 25.10 or later)

2. Create a new file named main.nf in your current directory

3. Copy and save the above script to your new file

4. Run your pipeline:

nextflow run main.nf

See Your first script for more information about this pipeline.