Workflow: ProGENI
Fetched 2023-01-13 21:23:32 GMT
Verified with cwltool version 3.1.20221201130942
network-guided gene prioritization method implementation by KnowEnG that ranks gene measurements by their correlation to observed phenotypes
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| taxonid | String (Optional) | Species TaxonID |
taxon id of species related to genomic spreadsheet |
| edge_type | String | Subnetwork Edge Type |
the edge type keyword for the subnetwork of interest |
| redis_host | String (Optional) | RedisDB host URL |
url of Redis db |
| redis_pass | String (Optional) | RedisDB AuthStr |
password for Redis db |
| redis_port | Integer (Optional) | RedisDB Port |
port for Redis db |
| use_network | Boolean | Use Network Flag |
whether or not to use a network for ProGENI |
| network_type | String | Subnetwork Class |
the type of subnetwork |
| num_bootstraps | Integer | Number of bootstraps |
number of types to sample the data and repeat the analysis |
| correlation_measure | String | Correlation Measure |
keyword for correlation metric, one of either ['t_test', 'pearson'] |
| genomic_spreadsheet_file | File | Genomic Spreadsheet |
the genomic spreadsheet input for the pipeline |
| phenotypic_spreadsheet_file | File | Phenotypic Spreadsheet |
spreadsheet of phenotypic data with samples as rows and phenotypes as columns |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gp_runner |
gp_runner.cwl
(CommandLineTool)
|
ProGENI |
network-guided gene prioritization method implementation by KnowEnG that ranks gene measurements by their correlation to observed phenotypes |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| params_yml | File | Configuration Parameter File |
contains the values used in analysis |
| gene_map_file | File (Optional) | Genomic Spreadsheet Map |
two columns for internal gene ids and original gene ids |
| gene_unmap_file | File (Optional) | Genomic Spreadsheet Unmapped Genes |
two columns for original gene ids and unmapped reason code |
| top_ranked_genes | File | Lists of Top Genes |
Lists of Top Genes |
| cleaning_log_file | File (Optional) | Cleaning Log File |
information on souce of errors for cleaning pipeline |
| cleaning_yml_file | File (Optional) | Cleanup Parameter File |
data cleaning parameters in yaml format |
| network_edge_file | File | Subnetwork Edge File |
4 column format for subnetwork for single edge type and species |
| ranked_genes_file | File | Ranked Genes File |
Ranked Genes File |
| clean_genomic_file | File (Optional) | Clean Genomic Spreadsheet |
matrix with gene names mapped and data cleaned |
| fetch_cmd_log_file | File | Fetch Command Log File |
Fetch Command Log File |
| top100_genes_matrix | File | top100 Genes File |
Membership spreadsheet with phenotype columns and gene rows |
| clean_phenotypic_file | File (Optional) | Clean Phenotypic Spreadsheet |
phenotype file prepared for pipeline |
https://w3id.org/cwl/view/git/c490b21749bdd56691f0acf0e5f3a1dddfebfeea/Dockstore.cwl
