build-nextflow-params

build-nextflow-params

This action will build nextflow parameter file templates for Viash workflows and components in a folder.

Usage

This action will look for viash configs for workflows and components in a directory, and will generate (nextflow parameter file templates)[https://www.nextflow.io/docs/latest/cli.html#run]. For workflows, the parameter files will saved next to the Viash config, for components will output to the target directory (see viash ns build). This component required Viash to be installed and available in $PATH. We recommend to use viash-actions/setup before you run build-nextflow-params.

Inputs available

It is required to set at least one argument for components or for worklows:

• components - optional. Location of the viash configurations for components. Will most often be a folder from a repository that has been cloned in a previous step of your workflow using checkout. Ex: example_repository/src.

• workflows - optional. Location of the viash configurations for workflows. Will most often be a folder from a repository that has been cloned in a previous step of your workflow using checkout. Ex: example_repository/workfows.

• token - Personal access token (PAT) used to fetch the viash tools repository.

• tools_version - optional. Release of Viash tools to use. Will use the latest release by default. Ex: main_build

Examples

name: demo of build-nextflow-params
on:
  pull_request:
jobs:
  demo:
    runs-on: ubuntu-latest
    
    steps:
    - uses: viash-io/viash-actions/setup@v2
    - uses: actions/checkout@v3
      with:
        fetch-depth: 0

    - name: Build nextflow parameter files
      uses: viash-io/viash-actions/build-nextflow-params@v2
      with:
        workflows: workflows
        token: ${{ secrets.GTHB_PAT }}
        tools_version: 'main_build'