cellgeni/nichecompass

subworkflow

NicheCompass training & analysis

spatial_atlas_building niche_identification niche_characterisation cell-cell_communication_inference spatial_reference_mapping deep-learning

Module Information

Repository: https://github.com/cellgeni/nf-modules/tree/main/subworkflows/sanger-cellgeni/nichecompass
Source: Sanger (cellgeni)
Organization: cellgeni
Authors: @ASUQ
Maintainers: @ASUQ

This subworkflow uses the following modules:

Name	Type	Description
ch_h5ad	file	The input channel containing the H5AD files Structure: [ val(meta), path(h5ad) ]

Name	Type	Description
nichecompass_dir	directory	Channel containing NicheCompass output folder Structure: [ val(meta), path(nichecompass_dir) ]
notebook	file	Channel containing NicheCompass output Jupyter notebook Structure: [ val(meta), path(notebook) ]
versions	file	File containing software versions Structure: [ path(versions.yml) ]

Include this subworkflow in your Nextflow pipeline:

include { NICHECOMPASS } from 'https://github.com/cellgeni/nf-modules/tree/main/subworkflows/sanger-cellgeni/nichecompass'