This pipeline performs peak calling for ATAC data (only cisTopic option is available at the moment)
main.nf
- the Nextflow pipeline that runs the whole pipelinemodules/
- a collection pipeline's of processes for different componentsmodules/pycistopic/main.nf
- a collection of processes for cisTopic component
workflows/
- a collection pipeline's of workflows for different componentsworkflows/pycistopic/main.nf
- a collection of processes for cisTopic component
bin
- a colection of python scriptsbin/colored_logger.py
- a custom python logger with colored outputbin/make_pseudobulk.py
- a script to make a pseubobulks from fragments filebin/peak_calling.py
- a script to call peaks for celltypes' pseudobulksbin/infer_consensus.py
- a script to infer consensus peaks from pseudobulks' peak calling resultsbin/create_cistopic.py
- script that creates cisTopic object from consensus.bed
and fragments files
nextflow.config
- the configuration script that controls everything
- --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)
- Perform peak calling
nextflow run main.nf --sample_table ./examples/samples.csv --celltypes examples/celltypes.csv
- Perform peak calling and additionally create a cisTopic object
nextflow run main.nf --sample_table ./examples/samples.csv --celltypes examples/celltypes.csv --cisTopicObject