mkref

Creates an index for use with Cell Ranger. 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`
`assembly`	Genome assembly (eg. mm10)	`string`
`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 extmkref multithreaded

Cell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

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