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Pipelines run a defined series of analysis steps across samples. Biomni can help prepare inputs and interpret results, while Nextflow coordinates the workflow on managed cloud compute. Phylo supports selected versioned pipelines from the nf-core community and compatible custom Nextflow workflows. Open Resources from the main navigation, select Tools, then choose the Nextflow filter to browse established pipelines available in your workspace.

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Prepare a run

In a task, add a pipeline from + Add → Resources and reference your input files with @. Ask Biomni to check the inputs and configuration. For example:
Before launch, review that:
  • the pipeline matches your analysis;
  • samples and metadata are correct; and
  • references and parameters fit your study.
You can also provide a custom workflow. Include its main.nf, required modules or config files, and input data. Ask Biomni to check the files and explain the workflow’s expected inputs and outputs.

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Monitor and review

In the task, you can follow:
  • overall and process-level progress;
  • logs and error details; and
  • reports and outputs when available.
If a run fails, ask Biomni to explain the error and suggest a next step. You may be able to resume completed work or need to correct the inputs and run again. Review completed outputs alongside the scientific results. Run details and output lineage can help identify which process produced a file. Keep the pipeline version, inputs, references, and parameters with your analysis. To explore the run lifecycle without your own sequencing files, ask Biomni to use the nf-core/rnaseq test profile:
Check that the method and parameters fit your research question. Validate new or modified workflows on representative data. Biomni can help prepare and interpret a run, but researchers remain responsible for reviewing the method and results. Nextflow is an open-source workflow system developed by Seqera and its contributor community. Biomni supports Nextflow and selected nf-core pipelines. Phylo and Biomni are independent products and are not affiliated with, sponsored by, or endorsed by Seqera or nf-core.