Workflow: scRNA-seq pipeline using Salmon and Alevin
Fetched 2025-04-29 11:51:11 GMT
Verified with cwltool version 3.1.20230201224320
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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 | |
| img_dir | Directory | Directory containing TIFF files | |
| threads | Integer | Number of threads for Salmon | |
| fastq_dir | Directory[] | Directory containing FASTQ files | |
| metadata_dir | Directory | Directory containing gpr file and metadata.tsv | |
| keep_all_barcodes | Boolean (Optional) | ||
| expected_cell_count | Integer (Optional) | ||
| visium_probe_set_version | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
salmon-rnaseq/steps/fastqc.cwl
(CommandLineTool)
|
Runs fastQC on each fastq file in fastq directory | |
| trim_reads |
steps/trim-reads.cwl
(CommandLineTool)
|
Trim FASTQ files | |
| annotate_cells |
salmon-rnaseq/steps/salmon-quantification/annotate-cells.cwl
(CommandLineTool)
|
Assay-specific annotation of cell barcodes after quantification | |
| quantification |
steps/quantification.cwl
(CommandLineTool)
|
Run BWA alignment tool on FASTQ input | |
| adjust_barcodes |
steps/adjust-barcodes.cwl
(CommandLineTool)
|
Assay-specific adjustment of cell barcodes | |
| scanpy_analysis |
salmon-rnaseq/steps/scanpy-analysis.cwl
(CommandLineTool)
|
Dimensionality reduction and clustering | |
| squidpy_analysis |
salmon-rnaseq/steps/squidpy-analysis.cwl
(CommandLineTool)
|
Dimensionality reduction and clustering | |
| 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 | |
| ripley_plot | File (Optional) | ||
| spatial_plot | File (Optional) | Slide-seq bead plot, colored by Leiden cluster | |
| dispersion_plot | File | Gene expression dispersion plot | |
| count_matrix_h5ad | File | Unfiltered count matrix from BWA and umi_tools, 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 | |
| co_occurrence_plot | File (Optional) | ||
| 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 |
| squidpy_spatial_plot | File (Optional) | ||
| centrality_scores_plot | File (Optional) | ||
| squidpy_annotated_h5ad | File (Optional) | ||
| interaction_matrix_plot | File (Optional) | ||
| marker_gene_plot_logreg | File | Cluster marker genes, logreg method | |
| marker_gene_plot_t_test | File | Cluster marker genes, t-test | |
| neighborhood_enrichment_plot | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/37af2055e751f8c8ca68757648f24ea290bf5291/pipeline.cwl
