Workflow: Running cellranger count and lineage inference

Fetched 2023-01-04 09:58:57 GMT
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Inputs

ID Type Title Doc
chemistry String (Optional)
reference Directory
sample_name String
fastq_directory Directory[]
lineage_min_cells Integer (Optional)
lineage_min_features Integer (Optional)
lineage_reference_data String

Steps

ID Runs Label Doc
count
../tools/cellranger_count.cwl (CommandLineTool)
Run Cell Ranger Count
lineage
../tools/cellmatch_lineage.cwl (CommandLineTool)
Running a script to identify lineage of cells

Outputs

ID Type Label Doc
counts_out_dir Directory
lineage_cellmatch_lineage_out_dir Directory
Permalink: https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/subworkflows/single_cell_rnaseq.cwl