cellgeni/postcode_decoding

subworkflow

Sort SAM/BAM/CRAM file

spatial transcriptomics decoding postcode probabilistic decoding

Module Information

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

This subworkflow uses the following modules:

Name	Type	Description
ch_profile	file	The input channel containing the spot/cell profile files Structure: [ val(meta), path(profile) ]
ch_tabular_codebook	file	The codebook in a tabular format Structure: [ val(meta), path(tab_codebook) ]
ch_readout_file	file	The input channel containing the readout file for MERFISH-like data Structure: [ val(meta), path(readout) ]
ch_R	int	The number of imaging round for the profile Structure: [ val(meta), 6 ]
ch_loc	file	The cell/pixel/spot locatisable tsv file Structure: [ val(meta), path(localisation) ]

Name	Type	Description
decoding_result	file	Channel containing decoded results Structure: [ val(meta), path(csv) ]
processed_profiles	file	Channel containing reformatted profile files Structure: [ val(meta), path(profile) ]
versions	file	File containing software versions Structure: [ path(versions.yml) ]

Include this subworkflow in your Nextflow pipeline:

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