Add instructions to get started

[tverbeiren]

Below is a proposal.

README:

• Point users to the user guidelines on the website
• Point contributors to the contributor guidelines
• Add a set of commands to quickly get started with modifying the pipeline, e.g.:

  # download viash and nextflow
  bin/init
  # download test resources
  bin/viash run src/download/sync_test_resources/config.vsh.yaml
  # run unit test for a certain component
  bin/viash_test --query pca
  # run a component on some data
  bin/viash run src/dimred/pca/config.vsh.yaml -- --input resources_test/pbmc_1k_v3_protein/mms.h5mu --output foo.h5mu

• Run a pipeline from the CLI
• Run a pipeline from nf-tower

Website:

• Contributor guide
  • Directory structure
  • Fetch Viash & Nextflow
  • Build components
  • Fetch test resources
  • Run tests
  • Create new components (refer to viash.io)
  • Create new pipelines (refer to viash.io)
• User guide (separate page, should not be in the contributors guide)
  • Run pipeline from CLI
  • Run pipeline from NF tower
  • Ingesting large param sets with param_list
  • To configure infrastructure related settings, create a profile with additional labels:
    • Setting resource constraints with labels (e.g. highmem, highcpu)
    • Singularity, Docker, ...?
    • Run on HPC cluster, cloud, ...
  • Deploying pipelines on premises -- get in touch?

[rcannood]

Extended proposed contents :)