Chapter 7 Params and config

This section includes some extra features related to params and the config file.

A full link of config info can be seen in the nextflow docs

7.1 Params

Workflow parameters can be set at the top of the primary main.nf file.

/*
 * Params
*/
params.dir = "."
params.outdir = "./results"
params.sample_name = "Sample_1"
params.fastqs = "/home/data/project123/raw_fastqs"
params.database = "/home/dbs/db123/db123.fastq"
params.conda_env = "/home/conda/envs/example_env"
params.rscript = "./rscripts/summary.rscript"

7.1.1 Params to channel

When using params containing a file in the workflow it is common practice to convert them to a channel.

workflow {
  database_ch = file(params.database)
}

More info/examples in Creating channels

7.2 Config

You can contain a lot of info in a config file.

Your primary config file should be in the same directory as your primary main.nf file and should be named nextflow.config. This will cause it to be used when you nextflow run main.nf -resume.

Link to nextflow configuration doc

7.2.1 Process directives

For Process directives you want to be the default of all processes in your workflow you can include them in your nextflow.config.

process {
  memory = 100.00GB
  cups = 8
  time = 30.d
}

7.2.2 Params in config

You can include your params in your config file.

params {
  dir = "."
  outdir = "./results"
  sample_name = "Sample_1"
  fastqs = "/home/data/project123/raw_fastqs"
  database = "/home/dbs/db123/db123.fastq"
  conda_env = "/home/conda/envs/example_env"
  rscript = "./rscripts/summary.rscript"
}

Ensure you still use params. as a prefix in the various .nf files.

7.2.3 Conda

Rather than needing to include -use-conda in your command line you can add the below to your nextflow.config to make your workflow use conda.

conda.enabled = true

7.2.4 Container program

There are many different container programs. Below are what you can add to the nextflow.config to get the different ones to work.

This includes setting the path to the image (if using one) and enabling the specific container program.

/// Docker
process.container = 'nextflow/examples:latest'
docker.enabled = true

/// Singularity
process.container = '/path/to/singularity.img'
singularity.enabled = true

If using one of them ensure you specify the containers in the variosu processes.

Link to container nextflow docs

7.2.5 Config profiles

You can have multiple profiles in a nextflow.config file.

To use a profile you would run:

nextflow run main.nf -profile laptop

To make different profiles you could include the below in your nextflow.config.

profiles {
    laptop {
        process.executor = 'local'
        docker.enabled = true
    }
    hpc {
        process.executor = 'slurm'
        conda.enabled = true
        process.resourceLimits = [
            memory: 750.GB,
            cpus: 200,
            time: 30.d
        ]
    }
}