Workflow: checker-workflow-wrapping-tool.cwl
Fetched 2023-01-12 06:44:48 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | 74e4371da0e7b7a159e0a24edfc09265[] | ||
| analysis | String[] | ||
| vrn_file | String[] | ||
| resources | String[] | ||
| description | String[] | ||
| rgnames__lb | String[] | ||
| rgnames__pl | String[] | ||
| rgnames__pu | String[] | ||
| rgnames__rg | String[] | ||
| genome_build | String[] | ||
| rgnames__lane | String[] | ||
| reference__rtg | File[] | ||
| metadata__batch | String[] | ||
| rgnames__sample | String[] | ||
| reference__twobit | File[] | ||
| expected_validation | File | ||
| metadata__phenotype | String[] | ||
| reference__versions | File[] | ||
| config__algorithm__qc | f83ba08b534ddfd0b152ccd1b7d95f49[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__genome_context | 908de523d0f727d87bd88421a5f5fa15[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 27ff2fd9a064854eb625a6ab91112fc2[] | ||
| config__algorithm__adapters | 57806d4fbc1b040249e0be48ad336c4e[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__svcaller | 23d696db1682620a88d1973c752c4218[] | ||
| config__algorithm__tools_on | 53045535e157847810e12e2d8d12d265[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | 7cfe43372695f13d2a39c157ae2d9676[] | ||
| reference__snpeff__GRCh37_75 | File[] | ||
| config__algorithm__svvalidate | String[] | ||
| config__algorithm__trim_reads | String[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__svprioritize | String[] | ||
| config__algorithm__variantcaller | 0dc19abada8baaa435cc66844aac7e9d[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__esp | File[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| genome_resources__variation__exac | File[] | ||
| config__algorithm__exclude_regions | 0048c3f11e7d35021fbf00a1b0c02b80[] | ||
| config__algorithm__mark_duplicates | Boolean[] | ||
| config__algorithm__variant_regions | File[] | ||
| genome_resources__aliases__ensembl | String[] | ||
| genome_resources__rnaseq__gene_bed | File[] | ||
| genome_resources__variation__1000g | File[] | ||
| genome_resources__variation__dbsnp | File[] | ||
| genome_resources__variation__polyx | File[] | ||
| config__algorithm__align_split_size | String[] | ||
| config__algorithm__nomap_split_size | Long[] | ||
| config__algorithm__validate_regions | File[] | ||
| genome_resources__variation__cosmic | File[] | ||
| config__algorithm__coverage_interval | String[] | ||
| genome_resources__variation__clinvar | File[] | ||
| config__algorithm__min_allele_fraction | Double[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__train_hapmap | File[] | ||
| genome_resources__variation__train_indels | File[] | ||
| genome_resources__variation__encode_blacklist | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| agha |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| workflow_output_file | File |
Permalink:
https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/wes-agha-test/checker-workflow-wrapping-tool.cwl
