Workflow: Single-Cell WNN Cluster Analysis
Fetched 2024-06-10 16:44:19 GMT
Verified with cwltool version 3.1.20230201224320
Single-Cell WNN Cluster Analysis Clusters cells by similarity on the basis of both gene expression and chromatin accessibility data from the outputs of the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” and “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipelines run sequentially. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, “Single-Cell Differential Abundance Analysis”, “Single-Cell ATAC-Seq Differential Accessibility Analysis”, and “Single-Cell ATAC-Seq Genome Coverage” pipelines.
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Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| alias | String | Analysis name | |
| threads | Cores/CPUs |
Parallelization parameter to define the number of cores/CPUs that can be utilized simultaneously. Default: 4 |
|
| resolution | Float (Optional) | Clustering resolution |
The resolution defines the “granularity” of the clustered data. Larger resolution values lead to more clusters. The optimal resolution often increases with the number of cells. Default: 0.3 |
| color_theme | Plots color theme |
Color theme for all plots saved as PNG files. Default: classic |
|
| query_data_rds | File | Single-cell Analysis with both PCA and LSI Transformed Datasets |
Analysis that includes single-cell multiome RNA and ATAC-Seq datasets run through both \"Single-Cell RNA-Seq Dimensionality Reduction Analysis\" and \"Single-Cell ATAC-Seq Dimensionality Reduction Analysis\" at any of the processing stages. |
| rna_dimensions | Integer (Optional) | Target RNA dimensionality |
Target RNA dimensionality is the number of principal components to be used in constructing the weighted nearest-neighbor graph before clustering. The accepted values range from 1 to 50. Default: 40 |
| atac_dimensions | Integer (Optional) | Target ATAC dimensionality |
Target ATAC dimensionality is the number of LSI dimensions to be used in constructing the weighted nearest-neighbor graph before clustering. The accepted values range from 2 to 50. The first dimension is always excluded. Default: 40 |
| genes_of_interest | String (Optional) | Genes of interest |
A comma- or space-separated list of genes of interest to visualize expression. If the “Cell Ranger RNA+ATAC Sample (optional)” input was provided the ATAC fragment coverage plots will be created as well. Default: None |
| atac_fragments_file | File (Optional) | Cell Ranger RNA+ATAC Sample (optional) |
Any \"Cell Ranger ATAC or RNA+ATAC Sample\" for generating ATAC fragments coverage plots over the genes of interest. This sample can be obtained from either \"Cell Ranger Count (RNA+ATAC)\" or \"Cell Ranger Aggregate (RNA+ATAC)\" pipeline |
| identify_diff_genes | Boolean (Optional) | Find gene markers |
The user can identify upregulated genes in each cluster compared to all other cells. The results include only genes that are expressed in at least 10% of the cells coming from either the current cluster or from all other clusters together. Genes with the log2FoldChange values smaller than 0.25 are excluded. The p-values are calculated with the Wilcoxon Rank Sum test and adjusted for multiple comparisons using the Bonferroni correction. Default: true |
| identify_diff_peaks | Boolean (Optional) | Find peak markers |
The user can identify differentially accessible peaks in each cluster compared to all other cells. The results include only peaks that are present in at least 5% of the cells coming from either the current cluster or from all other clusters together. Peaks with log2FoldChange values smaller than 0.25 are excluded. The p-values are calculated using the logistic regression framework and adjusted for multiple comparisons using the Bonferroni correction. Default: false |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sc_wnn_cluster |
../tools/sc-wnn-cluster.cwl
(CommandLineTool)
|
Single-Cell WNN Cluster Analysis |
Single-Cell WNN Cluster Analysis |
| compress_pdf_plots |
../tools/tar-compress.cwl
(CommandLineTool)
|
TAR compress |
TAR compress
========================================= |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| pdf_plots | File | Compressed folder with all PDF plots |
Compressed folder with all PDF plots. |
| seurat_data_rds | File | Seurat object in RDS format |
Seurat object. RDS format. |
| gene_markers_tsv | File (Optional) | Gene markers |
Gene markers. TSV format. |
| peak_markers_tsv | File (Optional) | Peak markers |
Peak markers. TSV format. |
| xpr_htmp_res_tsv | File[] (Optional) | Gene expression heatmap (top gene markers) |
Gene expression heatmap. Top gene markers. TSV format. |
| cvrg_res_plot_png | File[] (Optional) | ATAC fragment coverage (per gene) |
ATAC fragment coverage. All genes of interest. PNG format. |
| seurat_data_scope | File (Optional) | Seurat object in SCope compatible loom format |
Seurat object. SCope compatible. Loom format. |
| ucsc_cb_html_data | Directory (Optional) | UCSC Cell Browser (data) |
UCSC Cell Browser html data. |
| ucsc_cb_html_file | File (Optional) | UCSC Cell Browser |
UCSC Cell Browser html index. |
| xpr_avg_res_plot_png | File[] (Optional) | Average gene expression |
Average gene expression. PNG format. |
| xpr_dnst_res_plot_png | File[] (Optional) | Gene expression density (per gene) |
Gene expression density. All genes of interest. PNG format. |
| xpr_htmp_res_plot_png | File[] (Optional) | Gene expression heatmap (top gene markers) |
Gene expression heatmap. Top gene markers. PNG format. |
| xpr_per_cell_plot_png | File[] (Optional) | UMAP colored by gene expression (per gene) |
UMAP colored by gene expression. All genes of interest. PNG format. |
| sc_wnn_cluster_stderr_log | File | Error log |
Stderr log from the sc_wnn_cluster step. |
| sc_wnn_cluster_stdout_log | File | Output log |
Stdout log from the sc_wnn_cluster step. |
| umap_gr_clst_res_plot_png | File[] (Optional) | UMAP colored by cluster (all cells) |
UMAP colored by cluster. All cells. PNG format. |
| cmp_gr_ph_spl_cnd_plot_png | File (Optional) | Composition plot colored by cell cycle phase (split by grouping condition, downsampled) |
Composition plot colored by cell cycle phase. Split by grouping condition; first downsampled to the smallest dataset, then downsampled to the smallest group. PNG format. |
| cmp_gr_ph_spl_idnt_plot_png | File (Optional) | Composition plot colored by cell cycle phase (split by dataset, downsampled) |
Composition plot colored by cell cycle phase. Split by dataset; downsampled to the smallest dataset. PNG format |
| umap_gr_ph_spl_cnd_plot_png | File (Optional) | UMAP colored by cell cycle phase (split by grouping condition, downsampled) |
UMAP colored by cell cycle phase. Split by grouping condition; first downsampled to the smallest dataset, then downsampled to the smallest group. PNG format. |
| umap_gr_ph_spl_idnt_plot_png | File (Optional) | UMAP colored by cell cycle phase (split by dataset, downsampled) |
UMAP colored by cell cycle phase. Split by dataset; downsampled to the smallest dataset. PNG format. |
| cmp_gr_ph_spl_clst_res_plot_png | File[] (Optional) | Composition plot colored by cell cycle phase (split by cluster, optionally downsampled) |
Composition plot colored by cell cycle phase. Split by cluster; downsampled to the smallest dataset (if multiple datasets are analyzed jointly). PNG format |
| cmp_gr_clst_spl_cnd_res_plot_png | File[] (Optional) | Composition plot colored by cluster (split by grouping condition, downsampled) |
Composition plot colored by cluster. Split by grouping condition; first downsampled to the smallest dataset, then downsampled to the smallest group. PNG format. |
| umap_gr_clst_spl_ph_res_plot_png | File[] (Optional) | UMAP colored by cluster (split by cell cycle phase, optionally downsampled) |
UMAP colored by cluster. Split by cell cycle phase; downsampled to the smallest dataset (if multiple datasets are analyzed jointly). PNG format. |
| cmp_gr_clst_spl_idnt_res_plot_png | File[] (Optional) | Composition plot colored by cluster (split by dataset, downsampled) |
Composition plot colored by cluster. Split by dataset; downsampled to the smallest dataset. PNG format. |
| umap_gr_clst_spl_cnd_res_plot_png | File[] (Optional) | UMAP colored by cluster (split by grouping condition, downsampled) |
UMAP colored by cluster. Split by grouping condition; first downsampled to the smallest dataset, then downsampled to the smallest group. PNG format. |
| umap_gr_clst_spl_idnt_res_plot_png | File[] (Optional) | UMAP colored by cluster (split by dataset, downsampled) |
UMAP colored by cluster. Split by dataset; downsampled to the smallest dataset. PNG format. |
https://w3id.org/cwl/view/git/cc6fa135d04737fdde3b4414d6e214cf8c812f6e/workflows/sc-wnn-cluster.cwl
