A repository of pipelines for single-cell data analysis in Nextflow DSL2.

Full documentation is available on Read the Docs, or take a look at the Quick Start guide.

This main repo contains multiple workflows for analyzing single cell transcriptomics data, and depends on a number of tools, which are organized into subfolders within the src/ directory. The VIB-Singlecell-NF organization contains this main repo along with a collection of example runs (VSN-Pipelines-examples). Currently available workflows are listed below.

If VSN-Pipelines is useful for your research, consider citing:

• VSN-Pipelines All Versions (latest): 10.5281/zenodo.3703108.

These are set up to run Cell Ranger and DropSeq pipelines.

The Single Sample Workflows perform a "best practices" scRNA-seq analysis. Multiple samples can be run in parallel, treating each sample separately.

Single Sample Workflows

Pipeline / Entrypoint	Purpose	Documentation
single_sample	Independent samples
single_sample_scenic	Ind. samples + SCENIC
scenic	SCENIC GRN inference
scenic_multiruns	SCENIC run multiple times
single_sample_scenic_multiruns	Ind. samples + multi-SCENIC
single_sample_scrublet	Ind. samples + Scrublet
decontx	DecontX
single_sample_decontx	Ind. samples + DecontX
single_sample_decontx_scrublet	Ind. samples + DecontX + Scrublet

Sample Aggregation Workflows: perform a "best practices" scRNA-seq analysis on a merged and batch-corrected group of samples. Available batch correction methods include BBKNN, mnnCorrect, and Harmony.

Sample Aggregation Pipelines

Pipeline / Entrypoint	Purpose	Documentation
bbknn	Sample aggregation + BBKNN
bbknn_scenic	BBKNN + SCENIC
harmony	Sample aggregation + Harmony
harmony_scenic	Harmony + SCENIC
mnncorrect	Sample aggregation + mnnCorrect

In addition, the pySCENIC implementation of the SCENIC workflow is integrated here and can be run in conjunction with any of the above workflows. The output of each of the main workflows is a loom-format file, which is ready for import into the interactive single-cell web visualization tool SCope. In addition, data is also output in h5ad format, and reports are generated for the major pipeline steps.

Single cell ATAC-seq processing steps are now included in VSN Pipelines. Currently, a preprocesing workflow is available, which will take fastq inputs, apply barcode correction, read trimming, bwa mapping, and output bam and fragments files for further downstream analysis. See here for complete documentation.