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.
moduleInputs
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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