Workflow: AltAnalyze CellHarmony
Fetched 2023-01-09 13:04:11 GMT
Verified with cwltool version 3.1.20221201130942
AltAnalyze CellHarmony ======================
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| alias | String | Experiment short name/Alias | |
| align_by | Aligning algorithm |
Aligning to cluster centroid or cell |
|
| genome_data | Directory | AltAnalyze Prepare Genome Experiment |
Ensembl database from the altanalyze-prepare-genome.cwl pipeline |
| use_adjusted_pvalue | Boolean (Optional) | Use adjusted P-value for differentially expressed genes threshold |
Use adjusted P-value for differentially expressed genes threshold. Applied if running differential expression |
| correlation_threshold | Float (Optional) | Pearson correlation threshold |
Pearson correlation threshold |
| perform_diff_expression | Boolean (Optional) | Perform differential expression analysis |
Perform differential expression analysis |
| diff_expr_p_value_threshold | Float (Optional) | Cutoff value for P-value of P-adjusted-value |
Cutoff value for P-value of P-adjusted-value. Applied if running differential expression |
| filtered_feature_bc_matrix_h5 | File | scRNA-Seq Cell Ranger Experiment |
Filtered feature-barcode matrices in HDF5 format from cellranger count or aggr results |
| reference_marker_heatmap_file | File | AltAnalyze ICGS Experiment |
AltAnalyze ICGS Marker Gene Heatmap |
| diff_expr_fold_change_threshold | Float (Optional) | Differential expression fold-change threshold |
Differential expression fold-change threshold. Applied if running differential expression |
| reference_expression_matrix_file | File | AltAnalyze ICGS Experiment |
AltAnalyze ICGS Expression Matrix |
| reference_annotation_metadata_file | File | AltAnalyze ICGS Experiment |
AltAnalyze ICGS Annotation Metadata |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| altanalyze_cellharmony |
../tools/altanalyze-cellharmony.cwl
(CommandLineTool)
|
Runs AltAnalyze cellHarmony for 10X Genomics data |
|
| compress_cellharmony_data_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cellharmony_stderr_log | File | stderr log generated by altanalyze cellharmony |
stderr log generated by altanalyze cellharmony |
| cellharmony_stdout_log | File | stdout log generated by altanalyze cellharmony |
stdout log generated by altanalyze cellharmony |
| compressed_cellharmony_data_folder | File | Compressed folder with AltAnalyze CellHarmony results |
Compressed folder with AltAnalyze CellHarmony results |
https://w3id.org/cwl/view/git/480e99a4bb3046e0565113d9dca294e0895d3b0c/workflows/altanalyze-cellharmony.cwl
