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Pipeline Guide

Foundry supports both Via and nf-core/Nextflow pipelines. This section explains how to export pipelines from Foundry to a remote Git/Bitbucket/Gitlab repository.

Exporting Via and nf-core/Nextflow Pipelines

You can export both Via and nf-core/Nextflow pipelines from Foundry using the same workflow:

  1. Go to the Pipelines page and select the pipeline you want to export.
  2. Click the three-dot (⋮) menu in the top-right corner and choose Export Pipeline.
  3. Select the repository credentials you configured under Profile → Integration Tokens.
  4. Enter the Repository URL (for example, https://github.com/your-org/your-pipeline).
  5. (Optional) Enter the tag/branch you want to use (for example, main or 3.6.1).
  6. Click Export Pipeline to start the export.

For Via pipelines, Foundry:

  • Generates an extra importable .vf file representing the pipeline.
  • Pushes this .vf file to the selected repository using the credentials and repository URL you provided.

These exported .vf files can later be re-imported into Foundry using the Via pipeline import flow.

Exporting Pipeline Parameters

To facilitate the exporting of used parameters in a pipeline, we have implemented a process called publish_params_as_JSON. This process can be found by using the search bar on the pipeline page. To enable this capability in a specific pipeline, you can simply drag and drop the publish_params_as_JSON process into the desired location.

Once you have added the process to the pipeline, please drag and drop the output parameter to the workflow and rename it as logs.

After the run completes, a file named run_params.json will be generated under the "logs" folder, containing the exported parameters.

[
    {
        "Adapter_Removal": {
            "min_length" : 11, 
            "Adapter_Sequence":"AGATCGGAAGAGC"
        },
        "bed": "s3://viafoundry/genome_data/mouse/mm10/refseq/genes/genes.bed", 
        "hisat2Index": "s3://viafoundry/genome_data/mouse/mm10/refseq/Hisat2Index", 
        "outdir": "s3://viafoundry/runs/report159"
    }
]