Workflow: facets-workflow.cwl
Fetched 2023-01-03 21:51:21 GMT
Verified with cwltool version 3.1.20221201130942
Workflow for running Facets-suite on a set of tumor normal pairs This workflow scatters over all the pairs in the input JSON to run all samples in parallel Input JSON format ----------------- { \"pairs\": [ { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal1.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.Normal1.maf\" }, \"pair_id\": \"Tumor1.Normal1\" }, { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal2.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.Normal2.maf\" }, \"pair_id\": \"Tumor2.Normal2\" } ] } Output format ------------- output └── facets-suite ├── Tumor1.Normal1.arm_level.txt ├── Tumor1.Normal1.gene_level.txt ├── Tumor1.Normal1_hisens.ccf.maf ├── Tumor1.Normal1_hisens.rds ├── Tumor1.Normal1_hisens.seg ├── Tumor1.Normal1_purity.rds ├── Tumor1.Normal1_purity.seg ├── Tumor1.Normal1.qc.txt ├── Tumor1.Normal1.snp_pileup.gz ├── Tumor1.Normal1.txt ├── Tumor2.Normal2.arm_level.txt ├── Tumor2.Normal2.gene_level.txt ├── Tumor2.Normal2_hisens.ccf.maf ├── Tumor2.Normal2_hisens.rds ├── Tumor2.Normal2_hisens.seg ├── Tumor2.Normal2_purity.rds ├── Tumor2.Normal2_purity.seg ├── Tumor2.Normal2.qc.txt ├── Tumor2.Normal2.snp_pileup.gz ├── Tumor2.Normal2.txt └── logs ├── success └── failed
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| pairs | 4461c84ab22d9587052f0a707ced064d[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| facets_suite |
facets-suite-workflow.cwl
(Workflow)
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Workflow for running the facets suite workflow on a single tumor normal pair Includes handling of errors in case execution fails for the sample pair |
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| check_facets_suite |
facets-workflow.cwl#check_facets_suite/check_facets_suite
(ExpressionTool)
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Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| qc_txt | File[] | ||
| facets_txt | File[] | ||
| hisens_rds | File[] | ||
| hisens_seg | File[] | ||
| output_dir | Directory | ||
| purity_rds | File[] | ||
| purity_seg | File[] | ||
| failed_pairs | String[] | ||
| annotated_maf | File[] | ||
| arm_level_txt | File[] | ||
| gene_level_txt | File[] | ||
| hisens_cncf_txt | File[] |
https://w3id.org/cwl/view/git/7eb2b0a4d37018142233d770595ac2e00376dab4/cwl/facets-workflow.cwl
