Workflow: Single-cell Reference Indices

Fetched 2023-03-26 21:41:02 GMT

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

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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

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

Builds Cell Ranger compatible reference folder from the custom genome FASTA and gene GTF annotation files.

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

Builds Cell Ranger ARC compatible reference folder from the custom genome FASTA and gene GTF annotation files.

Notes: - `input_motifs` parameter in the `config.txt` file is not implemented. - if GTF file provided in `annotation_gtf_file` has records with duplicate gene_id, they should be grouped together. Applicable to USCS RefGene annotations.

Outputs

ID Type Label Doc
stderr_log File

stderr log generated by cellranger mkref

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

Permalink: https://w3id.org/cwl/view/git/8614e5d20f5e81dce537216bd340cdbc1067bbc7/workflows/sc-ref-indices-wf.cwl