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Aligns and quantifies FastQ files from a 10X snRNA+ATAC-seq experiment against a reference genome. Output matrices are provided in triplet and h5 formats.

module

Inputs

Channel name	Description	Type
`opt`	A map of task-specific variables.	`map`
`tag`	An identifier to use in the tag directive.	`string`
`id`	Directory-safe name for the output directory.	`string`
`description`	A short description of the sample.	`string`
`samples`	An array of length two: RNA and chromatin assay sample names.	`string array`
`index_path`	Path to the properly-formatted index directory.	`path`
`all_libraries.csv`	Path to the liraries sample sheet. This will be searched using `grep` for the relevant samples.	`file`

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`
`libraries`	CSV-formatted file of the libraries used by the task.	`file`	`libraries.csv`
`quantification_path`	Cell Ranger outputs (`outs/`) directory.	`path`	`<id>/outs`
`atac_summary`	HTML summary for the ATAC-seq assay.	`file`	`atac_summary.html`
`joint_summary`	HTML summary for the joint RNA- and ATAC-seq assays.	`file`	`joint_summary.html`
`rna_summary`	HTML summary for the RNA-seq assay.	`file`	`rna_summary.html`

Tools

cell ranger arc extcount 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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