single_snake_sequencing - sc/snRNAseq Snakemake Workflow
A Snakemake workflow for standardised sc/snRNAseq analysis.
Every single cell analysis is slightly different. This represents what I would call a "core" analysis, as nearly every analysis I perform start with something very akin to this. Given this custom nature of single cell, this workflow is not designed to be all encompassing. Rather, it aims to be extensible, modular, and reproducible. Any given step can be easily modified - as they are all self contained scripts - and a new rule can be easily added - see the downstream rules for an example. Finally, by taking advantage of the integrated Conda and Singularity support, we can run the whole thing in an isolated environment.
Notes on Installation
HOLDING
Notes on Configuration
⚠️ Be sure to change the configuration to suit your project!
For a full discussion of configuration, please see the configuration README.
Briefly, the general configuration file must be located at config/config.yaml. A samplesheet containing information pertaining to the data must be supplied as well. Both are schema validated.
Notes on Data
This pipeline expects de-multiplexed fastq.gz files, normally produced by some deriviative of bcl2fastq after sequencing. They can (technically) be placed anywhere, but we recommend creating a data directory in your project for them.
Notes on the tools
The analysis pipeline was run using Snakemake v6.6.1. The full version and software lists can be found under the relevant yaml files in workflow/envs. The all reasonable efforts have been made to ensure that the repository adheres to the best practices outlined here.
Notes on the analysis
For a full discussion on the analysis methods, please see the technical documentation.
Briefly, the count matrix was produced using Cellranger, droplet calling with DropletUtils::emptyDrops, doublet detection with SOLO from the scVI family, batch effect removal with harmonypy, and general analysis and data handling with scanpy.
Future work
- Supply tests
- Track lane in samples that have been pooled and de-multiplexed
- Parallelise emptyDrops
- Support custom references
- Support SCTransform?
180 Oct 8, 2022
552 Dec 19, 2022
89 Jan 8, 2023
1.2k Dec 30, 2022
301 Dec 28, 2022
11 Nov 16, 2022
1 Oct 21, 2021
2 Nov 12, 2021
14 Dec 25, 2022
0 Dec 07, 2021
407 Nov 17, 2022
3 Feb 21, 2022
4 Oct 27, 2022
245 Dec 30, 2022
0 May 03, 2022
33 Jan 29, 2022
6 Oct 17, 2022
40 Nov 07, 2022
10 Nov 04, 2022
9 Apr 29, 2022
2 Jan 18, 2022
1 Nov 03, 2021
217 Dec 25, 2022
9 Jul 12, 2022
97 Dec 07, 2022
5 Dec 24, 2021
10 Jan 23, 2022
90 Dec 16, 2022
1 Feb 17, 2022