Workflow: Running cellranger count and lineage inference

Fetched 2023-01-10 01:58:34 GMT
children parents
workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs lineage_min_cells lineage_min_cells lineage Running a script to identify lineage of cells lineage_min_cells->lineage lineage_min_cells chemistry chemistry count Run Cell Ranger Count chemistry->count chemistry lineage_reference_data lineage_reference_data lineage_reference_data->lineage lineage_reference_data fastq_directory fastq_directory fastq_directory->count fastq_directory reference reference reference->count reference sample_name sample_name sample_name->count sample_name sample_name->lineage sample_name lineage_min_features lineage_min_features lineage_min_features->lineage lineage_min_features counts_out_dir counts_out_dir lineage_cellmatch_lineage_out_dir lineage_cellmatch_lineage_out_dir count->counts_out_dir count->lineage cellranger_out_dir lineage->lineage_cellmatch_lineage_out_dir
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

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
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/2decd55996b912feb48be5db1b052aa3274ee405/definitions/subworkflows/single_cell_rnaseq.cwl