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Nextflow

Nextflow is a free and open-source software distributed under the Apache 2.0 licence, developed by Seqera Labs. The software is used by scientists and engineers to write, deploy and share data-intensive, highly scalable, workflows on any infrastructure.

Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters

Note

nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow.

Interactive Usage

After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:

srun --pty bash -i

The latest version of Nextflow (currently version 23.10.0) is made available with the commands:

module load Nextflow/23.10.0

Note: The module file also loads Java/11.0.16

You can now run the nextflow command:

  $ nextflow -version
    N E X T F L O W
    version 23.10.0 build 5891
    created 15-10-2023 15:14 UTC (16:14 BST)
    cite doi:10.1038/nbt.3820
    http://nextflow.io

A Simple Script

Write a file named tutorial.nf (source) with the following content:

params.str = 'Hello world!'

process splitLetters {
  output:
    path 'chunk_*'

  """
  printf '${params.str}' | split -b 6 - chunk_
  """
}

process convertToUpper {
  input:
    path x
  output:
    stdout

  """
  cat $x | tr '[a-z]' '[A-Z]'
  """
}

workflow {
  splitLetters | flatten | convertToUpper | view { it.trim() }
}

Execute the script by entering the following command in your terminal:

$ nextflow run tutorial.nf

It will output something similar to the text shown below:

N E X T F L O W  ~  version 23.10.0
executor >  local (3)
[69/c8ea4a] process > splitLetters   [100%] 1 of 1 ✔
[84/c8b7f1] process > convertToUpper [100%] 2 of 2 ✔
WORLD!
HELLO

Batch usage

Ensure you have produced the above tutorial.nf script then write a file named batch.sh with the following content:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --mem=1000
#SBATCH --job-name=tutorial_smp_2
#SBATCH --output=tutorial_smp_2.out
#SBATCH --time=00:01:00
#SBATCH --mail-user=a.person@sheffield.ac.uk
#SBATCH --mail-type=ALL
module load Nextflow/23.10.0
nextflow run tutorial.nf

You can now submit this job to the SLURM scheduler with:

$ sbatch batch.sh

Your output file content will be similar to the following:

N E X T F L O W  ~  version 23.10.0
Launching `tutorial.nf` [peaceful_lamarr] DSL2 - revision: e61bd183fe
[-        ] process > splitLetters -

[-        ] process > splitLetters   [  0%] 0 of 1
[-        ] process > convertToUpper -

executor >  local (1)
[03/d6ce85] process > splitLetters   [100%] 1 of 1 ✔
[-        ] process > convertToUpper -

executor >  local (3)
[03/d6ce85] process > splitLetters       [100%] 1 of 1 ✔
[ff/dadc3e] process > convertToUpper (2) [100%] 2 of 2 ✔
HELLO
WORLD!

Installation notes

Installation method

This section is primarily for administrators of the system. Nextflow has been installed using the default Easybuild config files.

Build logs and test reports can be found in $EBDEVELNEXTFLOW with a given module loaded.

Testing method

Testing has been conducted with the above examples.