CTG singleCellWorkflows

Introduction

Here are the single cell pipelines used by Center For Translational Genomics (CTG). They are built according to the official documentations provided by 10X genomics.

This pipeline does not do any parsing of input. We use our samplesheet generator to create and parse valid samplesheets.

Status for workflows

Quick start

In production:

nextflow run main.nf --samplesheet </path/to/your/samplesheet.csv>

If you are using custom references:

nextflow run main.nf --samplesheet </path/to/your/samplesheet.csv> --custom_genome </path/to/custome_genome>

If you are not from ctg and don't want to run it with our ctg specific modules add --ctg_mode false like in:

nextflow run main.nf --samplesheet </path/to/your/samplesheet.csv> --custom_genome </path/to/custome_genome> --ctg_mode false

Testing:

nextflow run main.nf --samplesheet examples/CTG_SampleSheet.csv  \
    --outdir <local/output/directory> \
    -profile local_dev -stub-run \

Overview of processes

More info

• Project Setup
• 10X RNA-seq pipeline
• 10X CiteSeq pipeline
• 10X Flex pipeline
• 10X VDJ pipeline
• 10X ATAC pipeline
• 10X Multiome pipeline
• 10X Visium pipeline
• Contribution guide