This is a Nextflow workflow to run analysis of ScaleBio single-cell CRISPR sequencing libraries. It processes data from sequencing reads to single-cell outputs (gene-count matrix, etc.), and QC reports.
- First install Nextflow (22.04 or later)
- Download this workflow to your machine
- Install dependencies
- Create a samples.csv table for your samples
- Create runParams.yml, specifying inputs and analysis options for your run
- Launch the workflow for your run
- Sequencing reads
- Path to the Illumina Sequencer RunFolder (bcl files)
- If you prefer to start from fastq files, generated outside (before) this workflow, see Fastq generation.
- samples.csv
- A .csv file listing all samples in the analysis, optionally split by RT barcode. See samples.csv.
- guides
- Path to folder containing guide sequences to be detected and quantified by the workflow. See guides.txt.
- allCells
- Path to folder containing ScaleRna allCells.csv output files, one for each sample to be analyzed for the CROP analysis. See allCells.csv.
- outDir
- Path to desired output directory for workflow analysis
The workflow produces per-sample QC reports (metrics.csv), a cell-by-guide umi count-matrix (guideTab.filtered.csv) and more; See Outputs for a full list.
Once the above inputs have been collected and dependancies installed, the workflow can be executed by the following:
nextflow run /PATH/TO/CROP -profile PROFILE -params-file /PATH/TO/runParams.yml --outDir output
See dependencies for the best PROFILE to use on your system.
Note that nextflow options are given with a single - (e.g. -profile), while workflow parameters (e.g. --outDir) are given with a double dash --.
See the Nextflow command-line documentation for the options to run nextflow on different systems (including HPC clusters and cloud compute).
Analysis parameters (inputs, options, etc.) can be defined either in a runParams.yml file or directly on the nextflow command-line. See analysisParameters for details on the options.
In addition to the analysis parameters, a user-specific nextflow configuration file can be used for system settings (compute and storage resources, resource limits, storage paths, etc.):
-c path/to/user.config
See Nextflow configuration for the way different configuration files, parameter files and the command-line interact.
Different options to provide all required dependencies are described here. Follow one approach there and then run nextflow with the corresponding -profile.
Nextflow itself supports running using AWS, Azure and Google Cloud.
In addition Nextflow tower offers another simple way to manage and execute nextflow workflows in Amazon AWS.
See the Change log
For License information see licenseNotice.md.
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