Running pipelines

Note

TODO: Fill in these sections.

  • Examples should be using an OpenPipelines release or the main_build branch.
  • Point to the “Components” tab

Installing Viash and Nextflow

Before you try running OpenPipelines, please install Viash and Nextflow first.

Running pipelines from the CLI

bin/nextflow run . \
  -main-script workflows/integration/multimodal_integration/main.nf \
  -profile docker \
  -resume 
  --publish_dir foo/
  --input "bar"
  --output "test.txt"

Running pipelines from Nextflow Tower

Using param_list to pass large parameter sets

Using Viash’s VDSL3 nextflow platform, an optional -param_list argument can be used to pass a large number of inputs to a workflow. Additionally, the pipeline parameter values can be set for each input to the workflow independently. A param_list can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob:

  • A csv file should have column names which correspond to the different arguments of this pipeline. Example: --param_list data.csv with columns id,input.
  • A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: --param_list data.json with contents [ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ].
  • A yaml blob can also be passed directly as a string. Example: --param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]".
  • A list of maps can be in a nextflow.config file, where the keys of each map corresponds to the arguments of the pipeline. Example in a nextflow.config file: param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ].

When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when param_list is a list of maps (as-is) or a yaml blob.

Using a param_list can be combined with setting parameters that are set for all parameter sets. These ‘gobal’ parameters will always be overwritten with their counterpart that was specified in a more specific manner for a single parameter set. For example, using --param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar'} ]" --input 'global.txt' will result in the following parameter sets being processed:

  • id: foo, input: foo.txt
  • id: bar, input: global.txt