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.

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@0.1.0'
}

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

Seqera Platform run URL

The plugin exposes the URL generated by Seqera Platform as a workflow function:

include { seqeraPlatformUrl } from 'plugin/nf-fl86'

workflow {
    def platformUrl = seqeraPlatformUrl()
    log.info "Seqera Platform run: ${platformUrl}"
}

Call seqeraPlatformUrl() inside the workflow block so that the nf-tower observer has registered the run first. It returns null when Platform monitoring is disabled or no run URL is available.

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@0.1.0 \
    --outdir 's3://scratch/TEST' \
    --sample_sheet ./sample_sheet.csv

License

nf-fl86 is licensed under the Apache License 2.0.