Publish

Publish an artifact and optionally rename with parameters

Info

ID: publish
Namespace: transfer

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 0.12.0 -latest \
  -main-script target/nextflow/transfer/publish/main.nf \
  --help

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "path/to/file"
# output: "$id.$key.output.output"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.0 -latest \
  -profile docker \
  -main-script target/nextflow/transfer/publish/main.nf \
  -params-file params.yaml
Note

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

Argument group

Arguments

Name Description Attributes
--input Input filename file, required
--output Output filename file, required

Authors

  • Toni Verbeiren (maintainer)