Skip to content
nf-neuro

Your pipeline from A to Z

Environment Setup

We recommend using VS Code and the development container. Follow the setup documentation. You should be working in a folder containing the github repo: nf-neuro-tutorial.

Explore the github repository structure

The tutorial folder is pre-configured with necessary files and directories. The config, tests, modules and subworkflows folders contain the pre-installed nf-neuro components, while the data folder contains the data provided for the tutorial. Before starting to play with the data and the code, we will review some of the major files and folders in the structure: nextflow.config, main.nf and the data folder.

Here the current structure:

  • Directorynf-neuro-tutorial
    • .devcontainer
    • Directoryconfig/
      • …
    • Directorydata/
      • …
    • Directorymodules/
      • …
    • Directorysubworkflows/
      • …
    • Directorytests/
      • …
    • .gitignore
    • .nf-core.yml
    • README.md
    • main.nf
    • modules.json
    • nextflow.config
    • nf-test.config

nextflow.config

The nextflow.config file defines execution parameters and default configurations. It also contains parameters that users can change when calling your pipeline (prefixed with params.). Here is an example of a basic nextflow.config file :

nextflow.config
profiles {
    docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
}


manifest {
    name            = 'scilus/nf-neuro-tutorial'
    description     = """nf-neuro-tutorial is a Nextflow pipeline for processing neuroimaging data."""
    version         = '0.1dev'
}


params.input      = false
params.output     = 'result'

The parameters defined with params. can be changed at execution by another nextflow.config file or by supplying them as arguments when calling the pipeline using nextflow run :

nextflow run main.nf --input /path/to/input --output /path/to/output

main.nf

This file is your pipeline execution file. It contains all modules and subworkflows you want to run, and the channels that define how data passes between them. This is also where you define how to fetch your input pipeline files. This can be done using a workflow definition called get_data.

main.nf
#!/usr/bin/env nextflow


workflow get_data {
    main:
        if ( !params.input ) {
            log.info "You must provide an input directory containing all files using:"
            log.info ""
            log.info "    --input=/path/to/[input]   Input directory containing the file needed"
            log.info "                        |"
            log.info "                        └-- Input"
            log.info "                             └-- participants.*"
            log.info ""
            error "Please resubmit your command with the previous file structure."
        }


        input = file(params.input)
        // ** Loading all files. ** //
        participants_channel = Channel.fromFilePairs("$input/participants.*", flat: true)
            { "participants_files" }


    emit:
        participants = participants_channel
}


workflow {
    // ** Now call your input workflow to fetch your files ** //
    data = get_data()
    data.participants.view()
}

Data

To keep things simple, we’ll consider you want to process a BIDS dataset that contains for one subject and session a DWI and a T1 image, as follows:

  • Directorydata
    • dataset_description.json
    • participants.json
    • participants.tsv
    • Directorysub-003
      • Directoryses-01
        • Directoryanat
          • sub-003_ses-01_T1w.json
          • sub-003_ses-01_T1w.nii.gz
        • Directorydwi
          • sub-003_ses-01_dir-AP_dwi.bval
          • sub-003_ses-01_dir-AP_dwi.bvec
          • sub-003_ses-01_dir-AP_dwi.json
          • sub-003_ses-01_dir-AP_dwi.nii.gz