Nextflow Registry | nf-core/cellranger/multi@0.0.0-3fc6d40

nf-core/cellranger/multi @ 0.0.0-3fc6d40

Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing.

align reference cellranger multiomics gene expression vdj antigen capture antibody capture crispr

Latest version: 0.0.0-3fc6d40

Total downloads: 7

Source: nf-core/modules

Authors: @klkeys

Maintainers: @klkeys

Summary

Get started

Add the following snippet to your workflow script to include this module.

include { CELLRANGER_MULTI } from 'nf-core/cellranger/multi'

License

MIT License

Process

`Name`	`CELLRANGER_MULTI`

Input 21 channels

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

#2 tuple

`meta_gex` map	Groovy Map containing sample information
`gex_fastqs` file	FASTQ files `*.fastq.gz`

#3 tuple

`meta_vdj` map	Groovy Map containing sample information
`vdj_fastqs` file	FASTQ files `*.fastq.gz`

#4 tuple

`meta_ab` map	Groovy Map containing sample information
`ab_fastqs` file	FASTQ files `*.fastq.gz`

#5 tuple

`meta_beam` map	Groovy Map containing sample information
`beam_fastqs` file	FASTQ files `*.fastq.gz`

#6 tuple

`meta_cmo` map	Groovy Map containing sample information
`cmo_fastqs` file	FASTQ files `*.fastq.gz`

#7 tuple

`meta_crispr` map	Groovy Map containing sample information
`crispr_fastqs` file	FASTQ files `*.fastq.gz`

`gex_reference` directory	Folder containing Cellranger gene expression reference. Can also be a gzipped tarball `*.tar.gz`

`gex_frna_probeset` file	Fixed RNA profiling information containing custom probes in CSV format `*.csv`

`gex_targetpanel` file	Declaration of the target panel for Targeted Gene Expression analysis `*.csv`

`vdj_reference` directory	Folder containing Cellranger V(D)J reference. Can also be a gzipped tarball `*.tar.gz`

`vdj_primer_index` file	List of custom V(D)J inner enrichment primers `*.csv`

`fb_reference` file	The Feature Barcodes used for reference in Feature Barcoding Analysis `*.csv`

`beam_antigen_panel` file	The BEAM manifest in Feature Barcode CSV format `*.csv`

`beam_control_panel` file	The BEAM antigens set to control status, with corresponding MHC alleles, in Feature Barcode CSV format `*.csv`

`cmo_reference` file	Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` option in Cellranger `*.csv`

`cmo_barcodes` file	A CSV file appended to the Cellranger multi config linking samples to CMO IDs `*.csv`

`cmo_barcode_assignment` file	A CSV file that specifies the barcode-sample assignment in Cell Multiplexing analysis `*.csv`

`frna_sampleinfo` file