Workflow: Single-cell Reference Indices
Single-cell Reference Indices Builds a Cell Ranger and Cell Ranger ARC compatible reference folders from the custom genome FASTA and gene GTF annotation files
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
threads | Integer (Optional) |
Number of threads for those steps that support multithreading |
|
memory_limit | Integer (Optional) |
Maximum memory used (GB). The same will be applied to virtual memory |
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genome_fasta_file | File |
Reference genome FASTA file that includes all chromosomes |
|
annotation_gtf_file | File |
Reference genome GTF annotation file that includes refGene and mitochondrial DNA annotations |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
cellranger_mkref |
../tools/cellranger-mkref.cwl
(CommandLineTool)
|
Cell Ranger Build Reference Indices |
Cell Ranger Build Reference Indices |
sort_annotation_gtf |
sc-ref-indices-wf.cwl#sort_annotation_gtf/24986087-5868-4b50-a9ad-520995bdfb91
(CommandLineTool)
|
||
cellranger_arc_mkref |
../tools/cellranger-arc-mkref.cwl
(CommandLineTool)
|
Cell Ranger ARC Build Reference Indices |
Cell Ranger ARC Build Reference Indices |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
stderr_log | File |
stderr log generated by cellranger mkref |
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stdout_log | File |
stdout log generated by cellranger mkref |
|
arc_stderr_log | File |
stderr log generated by cellranger-arc mkref |
|
arc_stdout_log | File |
stdout log generated by cellranger-arc mkref |
|
indices_folder | Directory |
Cell Ranger reference genome indices folder |
|
arc_indices_folder | Directory |
Cell Ranger ARC reference genome indices folder |
https://w3id.org/cwl/view/git/8614e5d20f5e81dce537216bd340cdbc1067bbc7/workflows/sc-ref-indices-wf.cwl