Summary

nf-fl86 is a Nextflow plugin that prevents a fresh workflow run from using an output directory that already exists. It uses the legacy params.outdir value when one is provided and otherwise falls back to Nextflow's session.outputDir. The check is skipped only when Nextflow is actually resuming a previous run.

At startup, the plugin also copies the CSV referenced by params.sample_sheet to <outdir>/pipeline_info/sample_sheet.csv. If params.sample_sheet is not set, it falls back to params.input.

After a successful run, the plugin writes workflow metadata to <outdir>/pipeline_info/workflow.json and creates pipeline.complete in the Nextflow work directory.

An optional seqera_action {} block can launch a follow-up Seqera Action after a successful run, using an access token resolved from AWS Secrets Manager.

The plugin can also send non-fatal lifecycle updates to an HTTP endpoint for a Notion-backed run tracker. It sends one update when the workflow begins and a second update only after successful completion.

Get Started

nf-fl86 requires Nextflow 25.10.0 or later. Enable a published release in your pipeline's nextflow.config:

plugins {
    id 'nf-fl86@0.3.0'
}

Run the pipeline with a new output directory. The optional sample sheet is copied into the pipeline metadata directory:

nextflow run hello \
    --outdir 's3://scratch/TEST' \
    --sample_sheet ./sample_sheet.csv

If the output directory belongs to an earlier run that should be resumed, use Nextflow's -resume option. The plugin permits an existing output directory only when the Nextflow session is running in resume mode.

Examples

Follow-up Seqera Action

Configure a follow-up workflow launch directly in nextflow.config. The plugin resolves the access token from AWS Secrets Manager and launches the specified Seqera Action only after the current workflow succeeds:

seqera_action {
    aws_token_name = 'nextflow/secret'
    aws_region = 'us-east-1'
    run_name_suffix = '_quilt'
    action = '123456'
    workspace = '123456'
    params = '{"input":"s3://example-bucket/results"}'
}

No workflow.onComplete handler or script-level plugin import is required. The follow-up run name is the completed workflow's run name plus run_name_suffix. Set run_name instead when a fixed name is required.

params must be a JSON object string and is passed to Seqera as the follow-up workflow's parameters. If it is omitted, the plugin defaults to [input: params.outdir]; if params.outdir is not set, it uses Nextflow's resolved output directory. For example:

seqera_action {
    // Required settings omitted for brevity.
    params = '{"input":"s3://example-bucket/results","priority":"high"}'
}

The optional api_base setting selects an HTTPS Seqera Enterprise API origin. Missing configuration, AWS failures, and Seqera API failures are logged as warnings and do not change a successful workflow into a failed one. The token, secret value, and API response body are not logged.

Notion lifecycle updates

Configure endpoint templates in nextflow.config to update a Notion-backed run tracker automatically:

notion {
    beginning_endpoint = 'https://example.execute-api.us-east-2.amazonaws.com/prod/update-status-to-mapping-underway?ngsrun={NGSRUN}'
    complete_endpoint = 'https://example.execute-api.us-east-2.amazonaws.com/prod/update-status-to-mapped?ngsrun={NGSRUN}&seqeraPlatformUrl={seqeraPlatformUrl}'
}

Use single-quoted endpoint templates so the plugin replaces placeholders at runtime:

• {NGSRUN} is the first NGSRUN\d+ value in workflow.runName.
• {seqeraPlatformUrl} is the nf-tower watch URL, or empty when monitoring is unavailable. It is a Notion endpoint placeholder, not an exported workflow function.

Placeholder values are URL-encoded. Each endpoint is optional; the beginning endpoint runs at startup, while the completion endpoint runs only after a successful workflow. Requests use POST with X-HTTP-Method-Override: PATCH. Invalid configuration, absent run IDs, timeouts, connection errors, and non-2xx responses are logged without failing the workflow.

Command-line plugin selection

The plugin can also be selected on the command line instead of in nextflow.config:

nextflow run hello \
    -plugins nf-fl86@0.3.0 \
    --outdir 's3://scratch/TEST' \
    --sample_sheet ./sample_sheet.csv

License

nf-fl86 is licensed under the Apache License 2.0.