Workflow: scRNA-seq pipeline using Salmon and Alevin
Fetched 2023-01-10 08:36:36 GMT
Verified with cwltool version 3.1.20221201130942
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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 | String | scRNA-seq assay | |
| threads | Integer | Number of threads for Salmon | |
| fastq_dir | Directory[] | Directory containing FASTQ files | |
| expected_cell_count | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
steps/fastqc.cwl
(CommandLineTool)
|
Runs fastQC on each fastq file in fastq directory | |
| salmon |
steps/salmon.cwl
(CommandLineTool)
|
Run Salmon Alevin tool on FASTQ input | |
| trim_reads |
steps/trim-reads.cwl
(CommandLineTool)
|
Trim FASTQ files | |
| annotate_cells |
steps/annotate-cells.cwl
(CommandLineTool)
|
Assay-specific annotation of cell barcodes after quantification | |
| adjust_barcodes |
steps/adjust-barcodes.cwl
(CommandLineTool)
|
Assay-specific adjustment of cell barcodes | |
| scanpy_analysis |
steps/scanpy-analysis.cwl
(CommandLineTool)
|
Dimensionality reduction and clustering | |
| scvelo_analysis |
steps/scvelo-analysis.cwl
(CommandLineTool)
|
RNA velocity analysis via scVelo | |
| alevin_to_anndata |
steps/alevin-to-anndata.cwl
(CommandLineTool)
|
Convert Alevin sparse output to anndata.AnnData object, save as h5ad | |
| compute_qc_results |
steps/compute-qc-metrics.cwl
(CommandLineTool)
|
Compute QC metrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| qc_report | File | Quality control report in JSON format | |
| umap_plot | File | UMAP dimensionality reduction plot | |
| fastqc_dir | Directory[] | Directory of FastQC output files, mirroring input directory structure | |
| salmon_output | Directory | Full output of `salmon alevin` | |
| slideseq_plot | File (Optional) | Slide-seq bead plot, colored by Leiden cluster | |
| dispersion_plot | File | Gene expression dispersion plot | |
| raw_count_matrix | File | Unfiltered count matrix from Alevin, converted to H5AD, with intronic regions | |
| count_matrix_h5ad | File | Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts | |
| count_matrix_zarr | Directory | Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts | |
| scanpy_qc_results | File | Quality control metrics from Scanpy | |
| umap_density_plot | File | UMAP dimensionality reduction plot, colored by cell density | |
| filtered_data_h5ad | File | Full data set of filtered results |
Full data set of filtered results: expression matrix, coordinates in dimensionality-reduced space (PCA and UMAP), cluster assignments via the Leiden algorithm, and marker genes for one cluster vs. rest |
| filtered_data_zarr | Directory | Full data set of filtered results |
Full data set of filtered results: expression matrix, coordinates in dimensionality-reduced space (PCA and UMAP), cluster assignments via the Leiden algorithm, and marker genes for one cluster vs. rest |
| scvelo_annotated_h5ad | File | scVelo-annotated h5ad file, including cell RNA velocity | |
| scvelo_annotated_zarr | Directory | scVelo-annotated zarr directory, including cell RNA velocity | |
| marker_gene_plot_logreg | File | Cluster marker genes, logreg method | |
| marker_gene_plot_t_test | File | Cluster marker genes, t-test | |
| scvelo_embedding_grid_plot | File | scVelo velocity embedding grid plot | |
| scvelo_embedding_stream_plot | File (Optional) | scVelo velocity embedding stream plot |
Permalink:
https://w3id.org/cwl/view/git/ae58670c9a1d088583879c667aff50d9052d9b1d/pipeline.cwl
