cell_ranger
Use the 10X cellranger software to quantify expression and optionally create a genome index against which gene expression can be quantified.
Steps
Make genome index
Use cellranger mkref to make an index against which expression can be quantified using fasta file and gtf file. The output index is named using the id key.
Quantify expression
Run cellranger count to align and quantify gene expression using the FastQ files and a genome index.
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:tasks.
| Tag | Description |
|---|---|
:genome_indexes.missing | Datasets that do not have an index path, the unique set of indexes are created from fasta file and gtf file. |
:genome_indexes.provided | Datasets that have an index path so do not need further work. |
:index_paths | A channel of index paths for the genomes in the project. |
:datasets_to_quantify | Dataset parameters passed into the workflow, subset for relevant keys. |
:quantified_datasets | After quantification, the quantification path key is added to the parameters. |
:result | The new parameters from the workflow are merged back into the input parameters, with a quantification method key added. The channel is emitted from the workflow as result. |
:tasks | Each task’s output task.yaml files from the task channel. |