ATAC pipeline

This pipeline performs peak calling for ATAC data (only cisTopic option is available at the moment)

Contents of Repo

• main.nf - the Nextflow pipeline that runs the whole pipeline
• modules/ - a collection pipeline's of processes for different components
  • modules/pycistopic/main.nf - a collection of processes for cisTopic component
• workflows/ - a collection pipeline's of workflows for different components
  • workflows/pycistopic/main.nf - a collection of processes for cisTopic component
• bin - a colection of python scripts
  • bin/colored_logger.py - a custom python logger with colored output
  • bin/make_pseudobulk.py - a script to make a pseubobulks from fragments file
  • bin/peak_calling.py - a script to call peaks for celltypes' pseudobulks
  • bin/infer_consensus.py - a script to infer consensus peaks from pseudobulks' peak calling results
  • bin/create_cistopic.py - script that creates cisTopic object from consensus .bed and fragments files
• nextflow.config - the configuration script that controls everything

Pipeline Arguments

• --sample_table specify a .csv file with sample names and path to the CellRanger-arc output dir (see example below)
• --celltypes specify a .csv file with celltype annotation (must include 'sample_id', 'barcode' and 'celltype' colums)
• --cisTopicObject if specified the script creates cisTopicObject for each sample (otherwise only .bed files with consensus peaks are available)

Examples of use:

1. Perform peak calling

nextflow run main.nf --sample_table ./examples/samples.csv --celltypes examples/celltypes.csv

2. Perform peak calling and additionally create a cisTopic object

nextflow run main.nf --sample_table ./examples/samples.csv --celltypes examples/celltypes.csv --cisTopicObject