Run a VDSL3 module

Unlike typical Nextflow modules, VDSL3 modules can actually be used as a standalone pipeline.

To run a VDSL3 module as a standalone pipeline, you need to specify the input parameters and a --publish_dir parameter, as Nextflow will automatically choose the parameter names of the output files.

Viewing the help message

More information regarding a modules arguments can be shown by passing the --help parameter.

Example:

nextflow run target/nextflow/mycomponent/main.nf --help

Running a module as a standalone pipeline

You can run the executable by providing a value for each of the required arguments and --publish_dir (where output files are published).

Example:

nextflow run target/nextflow/mycomponent/main.nf \
  --input config.vsh.yaml \
  --publish_dir output/

Passing a parameter list

Every VDSL3 can accept a list of parameters to populate a Nextflow channel with. Assuming we want to process a set of input files in parallel, we can create a yaml file params.yaml containing the following information.

param_list:
  - id: sample1
    input: data/sample1.txt
  - id: sample2
    input: data/sample2.txt
  - id: sample3
    input: data/sample3.txt
  - id: sample4
    input: data/sample4.txt
arg1: 10
arg2: 5

You can run the pipeline on the list of parameters using the -params-file parameter.

nextflow run target/main.nf -params-file params.yaml --publish_dir output2

Tip

You can also pass a YAML, CSV or JSON file to the param_list parameter.