cell_ranger_arc

Using cellranger-arc software, libraries for snRNA-seq and cell-matched snATAC-seq assays are quantified against an index, which can be optionally created.

workflow

Steps

Create missing indexes

For datasets that do not have an index path, an index is created using the information in the genome stanza. The unique set of required indexes are created.

workflow:L28 cell_ranger_arc/mkref

Create project sample sheet

Write a formatted configuration file that includes all libraries in this project which will be subset for libraries in a dataset.

workflow:L65 cell_ranger_arc/make_libraries_csv

Quantify assays

Use the FastQ files to quantify RNA expression and chromatin accessibility in single cells.

workflow:L90 cell_ranger_arc/count

Printable channels

These channels can be dumped to the output device using the `-dump-channels` Nextflow option with the workflow root tag and the channel tag, for example: quantification:cell_ranger_arc:tasks.

Tag	Description
`:genome_indexes.missing`	Datasets for which the `index path` is missing; indexes will be created for these.
`:genome_indexes.provided`	Datasets for which the `index path` has been provided.
`:index_paths`	The indexes that have been created or provided.
`:feature_type_params`	A channel that collates the project-wide information required to make the Cell Ranger ARC sample sheet.
`:datasets_to_quantify`	Parameter sets for datasets that will be quantified.
`:quantified_datasets`	Parameter sets of datasets that were quantified.
`:result`	Input parameters with the `index path` (if applicable), `libraries_csv`, `quantification method` and `quantification path` keys added.
`:tasks`	Each task’s output `task.yaml` files from the `task` channel.