Generates a network from mermaid code


ID: mermaid
Namespace: report

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -main-script target/nextflow/report/mermaid/ \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "path/to/file"
# output: "$id.$key.output.output"
# output_format: "foo"
width: 800
height: 600
background_color: "white"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/report/mermaid/ \
  -params-file params.yaml

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group


Name Description Attributes
--input Input directory file, required
--output Generated network as output. file, required
--output_format Output format for the generated image. By default will be inferred from the extension of the file specified with –output. string
--width Width of the page integer, default: 800
--height Height of the page integer, default: 600
--background_color Background color for pngs/svgs (not pdfs) string, default: "white", example: "#F0F0F0"


  • Dries De Maeyer (maintainer)