Workflow: checker-workflow-wrapping-tool.cwl
Fetched 2023-01-12 01:58:03 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 | 6028fb4d66c85fd3b75733f470a05db8[] | ||
| 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 | c057dfbccb1d4d177fc2b58cb238c4fa[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__genome_context | ded1a5beec68425c1028a771e9eaeffd[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 1ac09d62e718bc7895f330ad23b2303f[] | ||
| config__algorithm__adapters | 015fb140ee87c689a09fc091fec4ef2c[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__svcaller | d0f8b9e53f25ca2604bf81eae9f61e78[] | ||
| config__algorithm__tools_on | e0ca33cc276132ff0f3f8b8f9fe767b5[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | d25ca8a737fd943ffce22e3a99ff1538[] | ||
| 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 | 48f998e4fe19b2b75abac11b6b1e13d1[] | ||
| 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 | 5f1218af0ff9f1859349f9289f0f5e94[] | ||
| 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/120b79b0a64d6e5bec1b00df9fb09d885a2f71a8/wes-agha-test/checker-workflow-wrapping-tool.cwl
