VSN-Pipelines

VSN-Pipelines has now been archived

2023-04-19 - Unfortunately due to lack of developers, VSN-pipelines is no longer being worked on and has been archived. The repo will remain in read-only mode from this point on.

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

Full documentation is available on Read the Docs <https://vsn-pipelines.readthedocs.io/en/latest/>, or take a look at the Quick Start <https://vsn-pipelines.readthedocs.io/en/latest/getting-started.html#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 <https://vsn-pipelines-examples.readthedocs.io/en/latest/>). 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 <https://doi.org/10.5281/zenodo.3703108>_.

Raw Data Processing Workflows

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

.. list-table:: Raw Data Processing Workflows :widths: 15 10 30 :header-rows: 1

* - Pipeline / Entrypoint
  - Purpose
  - Documentation
* - cellranger
  - Process 10x Chromium data
  - cellranger_
* - demuxlet_freemuxlet
  - Demultiplexing
  - demuxlet_freemuxlet_
* - nemesh
  - Process Drop-seq data
  - nemesh_

.. _cellranger: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#cellranger .. _demuxlet_freemuxlet: https://vsn-pipelines.readthedocs.io/en/develop/pipelines.html#demuxlet-freemuxlet .. _nemesh: https://vsn-pipelines.readthedocs.io/en/develop/pipelines.html#nemesh

Single Sample Workflows

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

.. list-table:: Single Sample Workflows :header-rows: 1

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

Sample Aggregation Workflows

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.

.. list-table:: Sample Aggregation Pipelines :widths: 15 10 30 :header-rows: 1

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

scATAC-seq workflows

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 <https://vsn-pipelines.readthedocs.io/en/latest/scatac-seq.html>_ for complete documentation.

.. |VSN-Pipelines| image:: https://img.shields.io/github/v/release/vib-singlecell-nf/vsn-pipelines :target: https://github.com/vib-singlecell-nf/vsn-pipelines/releases :alt: GitHub release (latest by date)

.. |ReadTheDocs| image:: https://readthedocs.org/projects/vsn-pipelines/badge/?version=latest :target: https://vsn-pipelines.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status

.. |Nextflow| image:: https://img.shields.io/badge/nextflow-21.04.3-brightgreen.svg :target: https://www.nextflow.io/ :alt: Nextflow

.. |Gitter| image:: https://badges.gitter.im/vib-singlecell-nf/community.svg :target: https://gitter.im/vib-singlecell-nf/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge :alt: Gitter

.. |Zenodo| image:: https://zenodo.org/badge/199477571.svg :target: https://zenodo.org/badge/latestdoi/199477571 :alt: Zenodo

.. _VIB-Singlecell-NF: https://github.com/vib-singlecell-nf .. _pySCENIC: https://github.com/aertslab/pySCENIC .. _SCENIC: https://aertslab.org/#scenic .. _loom: http://loompy.org/ .. _SCope: http://scope.aertslab.org/

.. |single_sample| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/single_sample/badge.svg :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#single-sample-single-sample :alt: Single-sample Pipeline

.. |single_sample_scenic| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/single_sample_scenic/badge.svg :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#single-sample-scenic-single-sample-scenic :alt: Single-sample SCENIC Pipeline

.. |scenic| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/scenic/badge.svg :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#scenic-scenic :alt: SCENIC Pipeline

.. |scenic_multiruns| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/scenic_multiruns/badge.svg :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#scenic-multiruns-scenic-multiruns-single-sample-scenic-multiruns :alt: SCENIC Multi-runs Pipeline

.. |single_sample_scenic_multiruns| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/single_sample_scenic_multiruns/badge.svg :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#scenic-multiruns-scenic-multiruns-single-sample-scenic-multiruns :alt: Single-sample SCENIC Multi-runs Pipeline

.. |single_sample_scrublet| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/single_sample_scrublet/badge.svg :target: https://vsn-pipelines.readthedocs.io/en/latest/pipelines.html#single-sample-scrublet-single-sample-scrublet :alt: Single-sample Scrublet Pipeline