Workflow: Complex DAG
Fetched 2023-01-11 22:44:24 GMT
Verified with cwltool version 3.1.20221201130942
Non-linear combination of KnowEnG tools
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| taxon | String | Subnetwork Species ID |
the taxonomic id for the species of interest |
| pheno_file | File | Phenotypic File |
spreadsheet of phenotypic data with samples as rows and phenotypes as columns |
| genomic_file | File | Genomic Spreadsheet File |
spreadsheet of genomic data with samples as columns and genes as rows |
| gg_edge_type | String | Subnetwork Edge Type |
the edge type keyword for the subnetwork of interest |
| pg_edge_types | String[] | Subnetwork Edge Type |
the edge type keyword for the subnetwork of interest |
| num_bootstraps | Integer | Number of bootstraps |
number of types to sample the data and repeat the analysis |
| correlation_method | String | Correlation Method |
keyword for correlation metric, i.e. t_test or pearson |
| num_clusters_array | Integer[] | Number of clusters |
number of subtypes to divide the samples into |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| clean_g |
sspp_runner.cwl
(CommandLineTool)
|
KN Spreadsheet Preprocessor |
Transforms user spreadsheet in preparation for KN analytics by removing noise, mapping gene names, and extracting metadata statistics |
| clean_p |
sspp_runner.cwl
(CommandLineTool)
|
KN Spreadsheet Preprocessor |
Transforms user spreadsheet in preparation for KN analytics by removing noise, mapping gene names, and extracting metadata statistics |
| clean_pt |
sspp_runner.cwl
(CommandLineTool)
|
KN Spreadsheet Preprocessor |
Transforms user spreadsheet in preparation for KN analytics by removing noise, mapping gene names, and extracting metadata statistics |
| ggkn_fetch |
knf_runner.cwl
(CommandLineTool)
|
Knowledge Network Fetcher |
Retrieve appropriate subnetwork from KnowEnG Knowledge Network from AWS S3 storage |
| gokn_fetch |
knf_runner.cwl
(CommandLineTool)
|
Knowledge Network Fetcher |
Retrieve appropriate subnetwork from KnowEnG Knowledge Network from AWS S3 storage |
| gp_netboot |
gp_runner.cwl
(CommandLineTool)
|
ProGENI |
Network-guided gene prioritization method implementation by KnowEnG that ranks gene measurements by their correlation to observed phenotypes. |
| enrichments |
workflow.gsc.cwl
(Workflow)
|
GSC Paired Jobs |
Serial combination of KnowEnG tools |
| gsc_go_drawr |
gsc_runner.cwl
(CommandLineTool)
|
Gene Set Characterization |
Network-guided gene set characterization method implementation by KnowEnG that relates public gene sets to user gene sets |
| top10_gather |
top10_runner.cwl
(CommandLineTool)
|
top10 |
Get the 10 rows with the smallest value in the selected column |
| clustering_wf |
workflow.sc.cwl
(Workflow)
|
SC w/ Evaluation |
Serial combination of KnowEnG tools |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gp_out | File | GP top100 Genes |
Membership spreadsheet with phenotype columns and gene rows |
| g_c_out | File | Cleaned Genomic Spread |
Spreadsheet with columns and row headers |
| p_c_out | File | Cleaned Pheno Spread |
Spreadsheet with columns and row headers |
| p_t_out | File | Transposed Pheno Spread |
Spreadsheet with columns and row headers |
| sc_ce_out | File[] | Cluster Eval Results |
Table with results of statistical tests between cluster membership and phenoyptes |
| gg_knf_out | File | GG KnowNet Edges |
4 column format for subnetwork for single edge type and species |
| go_gsc_out | File | GO GSC Scores |
Edge format file with first three columns (user gene set, public gene set, score) |
| go_knf_out | File | GO KnowNet Edges |
4 column format for subnetwork for single edge type and species |
| sc_map_out | File[] | Cluster Membership |
Assignment of samples to clusters |
| sc_ce_top10 | File | top10 clusters~pheno |
file with 10 rows with the smallest value from the selected column |
| other_gsc_out | File[] | GSC Scores |
Edge format file with first three columns (user gene set, public gene set, score) |
https://w3id.org/cwl/view/git/8ca52a8d2b76d91b7618032a22699c5be7d12c6c/code/workflow.cwl
