## 2024-09-03
# Fork Notes:
I noticed that the repository has been archived. Unfortunately, the most recent version does not run with the most up-to-date motif files.
Therefore, I produced a fork that can run the scenic module of this VSN-pipeline in both single-run and multi-run modes.
To do this, I borrowed two fixes from the ccasar/vsn-pipelines
fork. These allow the VSN-pipeline to run in single-run mode if skipReports = true
in the config.
To allow the multi-run aggregation to function, I made one further tweak.
These are small changes but can be tricky to come across and should save time for people who want to automatically use SCENIC multi-run mode with aggregation.
---
# Run Notes:
To run, produce an environment and install the following:
- Singularity: 3.8.6
- Nextflow: 21.04.03 (crucial)
Then, export, checking before and after:
locale
export LANG="C"
export LC_ALL="C"
locale
Then, pull the fork:
nextflow pull JamesHowie14/vsn-pipelines -r master
ls -l ~/.nextflow/assets/JamesHowie14/vsn-pipelines
Make Config:
nextflow config JamesHowie14/vsn-pipelines \
-profile scenic,scenic_multiruns,scenic_use_cistarget_motifs,scenic_use_cistarget_tracks,hg38,singularity > nf_CPUopt-Real-MultiRun.config
Then, edit the config:
container = 'aertslab/pyscenic_scanpy:0.12.1_1.9.1' #crucial
skipReports = true #crucial, for up-to-date feather files for the motifs/tracks
Then, run via:
nextflow -C nf_CPUopt-Real-MultiRun.config run JamesHowie14/vsn-pipelines -entry scenic -r master
This should allow you to run the VSN-pipeline implementation of pySCENIC for the single-run and crucially also the multip-run mode, with aggregation.
Note -- scenic reports fail, hence skipped. To make this work requires and edit of vsn-pipelines/src/scenic/bin/reports/scenic_report.ipynb
. Have have not looked at this, but see ccasar/vsn-pipelines fork for one attempt to fix this.
# JMH - Sept, 3rd, 2024
##
2023-04-19 - Unfortunately due to lack of developers, VSN-pipelines is no longer being worked on and has been archived.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, 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.
Pipeline / Entrypoint | Purpose | Documentation |
---|---|---|
cellranger | Process 10x Chromium data | cellranger |
demuxlet_freemuxlet | Demultiplexing | demuxlet_freemuxlet |
nemesh | Process Drop-seq data | nemesh |
The Single Sample Workflows perform a "best practices" scRNA-seq analysis. Multiple samples can be run in parallel, treating each sample separately.
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.
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.