Running Pipelines with flowbio

flowbio allows you to submit pipeline jobs. You must provide the name of the pipeline, the version of that pipeline to run, the version of Nextflow to use, any parameters, and any data input parameters:

Name
name
Type
string
Description
The name of the pipeline to run.
Name
version
Type
string
Description
The name of the specific version of the pipeline, such as "1.2".
Name
nextflow_version
Type
string
Description
The version of Nextflow to use, providing it is one supported by the instance of Flow being used.
Name
params
Type
dict
Description
Any string/integer parameters to pass.
Name
data_params
Type
dict
Description
The data inputs, as a mapping of parameter names to data IDs - e.g {"file1": "123", "file2": "456"}.
Name
sample_params
Type
dict
Description
The sample inputs, along with any extra columns of data - e.g. {"samples": {"25": {"antibody": "goodgen"}}}.
Name
genome
Type
ID
Description
The ID of the genome to associate the execution with, if any.

Submitting a pipeline run

  execution = client.run_pipeline(
      "RNA-Seq",
      "3.8.1",
      "23.04.3",
      params={"param1": "param2"},
      data_params={"fasta": "123456789"},
  )