VSN-Pipelines

April 19, 2023 · View on GitHub

VSN-Pipelines has now been archived

2023-04-19 - Unfortunately due to lack of developers, VSN-pipelines is no longer being worked on and has been archived.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