Workflow: multiome pipeline using Salmon and Alevin (HuBMAP scRNA-seq pipeline) and HuBMAP scATAC-seq pipeline
Fetched 2025-11-04 13:40:47 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU General Public License v3.0 only
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| assay_rna | String | RNA-seq assay | |
| assay_atac | String | ATAC-seq assay | |
| exclude_bam | Boolean (Optional) | ||
| threads_rna | Integer | Number of threads for Salmon | |
| threads_atac | Integer (Optional) | Number of threads for scATAC-seq | |
| fastq_dir_rna | Directory[] | Directory containing RNA-seq FASTQ files | |
| fastq_dir_atac | Directory[] | Directory containing ATAC-seq FASTQ files | |
| keep_all_barcodes | Boolean (Optional) | ||
| atac_metadata_file | File (Optional) | ||
| expected_cell_count | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| consolidate_counts |
steps/consolidate_counts.cwl
(CommandLineTool)
|
Consolidate RNA, ATAC-seq | |
| rna_quantification | Salmon quantification, FASTQ -> H5AD count matrix | ||
| atac_quantification | |||
| downstream_analysis |
steps/downstream.cwl
(CommandLineTool)
|
Downstream analysis for RNA and ATAC |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| mofa_model | File | Multi-omics factor analysis model | |
| muon_original_h5mu | File | Consolidated expression cell-by-gene, cell-by-bin | |
| muon_processed_h5mu | File | Processed version of raw expression for each modality | |
| rna_embedding_result | File | Leiden clustering result on rna modality | |
| atac_embedding_result | File | Leiden clustering result on atac modality | |
| joint_embedding_result | File | Leiden clustering result on joint modality |
Permalink:
https://w3id.org/cwl/view/git/999afe5b202578ecd8e38bedf3e4788a431e6a58/pipeline.cwl
