nf-core/provenancereport

Edit

Introduction

nf-core/provenancereport is a reporting pipeline that validates a samplesheet and renders reproducible Quarto reports. The samplesheet has two columns, id and path, where each row points to one input file. The pipeline stages all listed files into a single Quarto render and publishes the rendered report plus any generated artifacts.

The default workflow performs the following steps:

1. Validate and normalise the input samplesheet with nf-schema.
2. Resolve each path entry from the samplesheet as one input file.
3. Render one Quarto notebook with all listed files using the nf-core quartonotebook module.
4. Publish the generated HTML report, report artifacts, and standard Nextflow execution metadata.

Usage

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

id,path
counts,counts.tsv
metadata,metadata.tsv

Each row represents exactly one input file. The id value is included in params$input_ids, and path must point to a single file.

Now, you can run the pipeline using:

nextflow run nf-core/provenancereport \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

By default, the pipeline renders the bundled notebook in assets/provenance_report.qmd. To render your own custom Quarto notebook, provide --notebook custom_report.qmd.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/provenancereport was originally written by Peltzer, Sturm, Schwab.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on the Slack #provenancereport channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.