6.2 Adding a help section for the whole pipeline

In this example we also describe another good practice: the use of the --help parameter. At the beginning of the pipeline we can write:

params.help             = false    // this prevents a warning of undefined parameter

// this prints the input parameters
log.info """
BIOCORE@CRG - N F TESTPIPE  ~  version ${version}
=============================================
reads                           : ${params.reads}
"""

// this prints the help in case you use --help parameter in the command line and it stops the pipeline
if (params.help) {
    log.info 'This is the Biocore\'s NF test pipeline'
    log.info 'Enjoy!'
    log.info '\n'
    exit 1
}

so launching the pipeline with --help will show you just the parameters and the help.

nextflow run test2.nf --help

N E X T F L O W  ~  version 20.07.1
Launching `test2.nf` [mad_elion] - revision: e3a80b15a2
BIOCORE@CRG - N F TESTPIPE  ~  version 1.0
=============================================
reads                           : /home/ec2-user/git/CoursesCRG_Containers_Nextflow_May_2021/nextflow/nextflow/test2/../testdata/*.fastq.gz
This is the Biocore's NF test pipeline
Enjoy!