Workflow: Running cellranger count and lineage inference

Fetched 2023-01-10 00:22:33 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs lineage_reference_data lineage_reference_data lineage Running a script to identify lineage of cells lineage_reference_data->lineage lineage_reference_data sample_name sample_name count Run Cell Ranger Count sample_name->count sample_name sample_name->lineage sample_name chemistry chemistry chemistry->count chemistry lineage_min_features lineage_min_features lineage_min_features->lineage lineage_min_features lineage_min_cells lineage_min_cells lineage_min_cells->lineage lineage_min_cells reference reference reference->count reference fastq_directory fastq_directory fastq_directory->count fastq_directory lineage_cellmatch_lineage_out_dir lineage_cellmatch_lineage_out_dir counts_out_dir counts_out_dir count->counts_out_dir count->lineage cellranger_out_dir lineage->lineage_cellmatch_lineage_out_dir
Workflow as SVG
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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
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Permalink: https://w3id.org/cwl/view/git/3a822294da63b4e19446a285e2fef075e23cf3d0/definitions/subworkflows/single_cell_rnaseq.cwl