mkref

Creates an index for use with Cell Ranger ARC. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.

module

Inputs

Channel name	Description	Type
`opt`	A map of task-specific variables.	`map`
`tag`	An identifier to use in the tag directive.	`string`
`organism`	Name of the organism (eg. Mus_musculus)	`string`
`assembly`	Genome assembly (eg. mm10)	`string`
`mon-nuclear contigs`	An array of chromosome names present in the FastA and GTF files that are not in the nucleus and therefore lack chromatin structure.	`strings`
`motifs`	Path to the transcription factor motifs in JASPAR format.	`file`
`path to FastAs`	Path to directory containing FastA files to index. These will be concatenated into a single FastA file.	`path`
`path to GTFs`	Path to directory containing GTF files. These will be concatenated into a single GTF file.	`path`

Outputs

Emission name	Description	Type	Filename pattern
`opt`	A map of task-specific variables.	`map`
`task`	YAML-formatted file of task parameters and software versions used by the task.	`file`	`task.yaml`
`path`	Path to the newly created index.	`path`

Tools

cell ranger arc multithreaded

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage. Furthermore, since the ATAC and GEX measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and GEX.

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