Workflow: AltAnalyze Iterative Clustering and Guide-gene Selection
Fetched 2023-04-08 04:48:19 GMT
Verified with cwltool version 3.1.20230201224320
Devel version of AltAnalyze Iterative Clustering and Guide-gene Selection =========================================================================
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| alias | String | Experiment short name/Alias | |
| downsample | Integer (Optional) | Downsample to |
Downsample to |
| genome_data | Directory | AltAnalyze Prepare Genome Experiment |
Ensembl database from the altanalyze-prepare-genome.cwl pipeline |
| restrict_by | Restrict by |
Restrict by |
|
| remove_outliers | Boolean (Optional) | Remove outliers |
Remove outliers |
| exclude_cell_cycle | Boolean (Optional) | Exclude cell cycle |
Exclude cell cycle |
| marker_pearson_cutoff | Float (Optional) | Marker Pearson cutoff |
Marker Pearson cutoff |
| raw_feature_bc_matrices_h5 | File | scRNA-Seq Cell Ranger Experiment |
Unfiltered feature-barcode matrices in HDF5 format from cellranger count or aggr results |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| altanalyze_icgs |
../tools/altanalyze-icgs.cwl
(CommandLineTool)
|
Runs AltAnalyze Iterative Clustering and Guide-gene Selection for 10X Genomics data |
|
| cellbrowser_build |
../tools/cellbrowser-build.cwl
(CommandLineTool)
|
Converts AltAnalyze outputs into the data structure supported by UCSC CellBrowser |
|
| compress_html_data_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
|
| compress_icgs_data_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| html_data_folder | Directory | Folder with not compressed CellBrowser formatted results |
Folder with not compressed CellBrowser formatted results |
| cellbrowser_report | File | CellBrowser formatted AltAnalyze ICGS report |
CellBrowser formatted AltAnalyze ICGS report |
| altanalyze_icgs_stderr_log | File | stderr log generated by altanalyze icgs |
stderr log generated by altanalyze icgs |
| altanalyze_icgs_stdout_log | File | stdout log generated by altanalyze icgs |
stdout log generated by altanalyze icgs |
| compressed_html_data_folder | File | Compressed folder with CellBrowser formatted results |
Compressed folder with CellBrowser formatted results |
| compressed_icgs_data_folder | File | Compressed folder with AltAnalyze ICGS results |
Compressed folder with AltAnalyze ICGS results |
https://w3id.org/cwl/view/git/a1f6ca50fcb0881781b3ba0306dd61ebf555eaba/workflows/altanalyze-icgs.cwl
