Workflow: main-wes_chr21_test.cwl
Fetched 2023-01-12 07:07:15 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 | 5325ddae2cc6a6de7af287c8c1fa0258[] | ||
| 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[] | ||
| metadata__phenotype | String[] | ||
| reference__versions | File[] | ||
| config__algorithm__qc | 52546bd43eee65cb6c1d5e082a4ac3e3[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__genome_context | 32272933eee319f492a90fc18dc77ed6[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 1c08902368a258960496a7698a65125f[] | ||
| config__algorithm__adapters | 38978d248e3dcaa179d3d7d898f1fd23[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__svcaller | 07d0336402d731cf335560d84ec5c372[] | ||
| config__algorithm__tools_on | 0cd6c07576d2d301346fd26adad03ad1[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | 629243f65ca0717b6b96cbf52e7e5e15[] | ||
| 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 | 230b1becb763fc610e3e4dd574f5dd59[] | ||
| 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 | f698b254c4d7742d097859638cc7aeec[] | ||
| 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 |
|---|---|---|---|
| svcall |
wf-svcall.cwl
(Workflow)
|
||
| alignment |
wf-alignment.cwl
(Workflow)
|
||
| qc_to_rec |
steps/qc_to_rec.cwl
(CommandLineTool)
|
||
| variantcall |
wf-variantcall.cwl
(Workflow)
|
||
| batch_for_sv |
steps/batch_for_sv.cwl
(CommandLineTool)
|
||
| prep_samples |
steps/prep_samples.cwl
(CommandLineTool)
|
||
| summarize_sv |
steps/summarize_sv.cwl
(CommandLineTool)
|
||
| summarize_vc |
steps/summarize_vc.cwl
(CommandLineTool)
|
||
| combine_calls |
steps/combine_calls.cwl
(CommandLineTool)
|
||
| multiqc_summary |
steps/multiqc_summary.cwl
(CommandLineTool)
|
||
| alignment_to_rec |
steps/alignment_to_rec.cwl
(CommandLineTool)
|
||
| pipeline_summary |
steps/pipeline_summary.cwl
(CommandLineTool)
|
||
| calculate_sv_bins |
steps/calculate_sv_bins.cwl
(CommandLineTool)
|
||
| batch_for_ensemble |
steps/batch_for_ensemble.cwl
(CommandLineTool)
|
||
| prep_samples_to_rec |
steps/prep_samples_to_rec.cwl
(CommandLineTool)
|
||
| batch_for_variantcall |
steps/batch_for_variantcall.cwl
(CommandLineTool)
|
||
| calculate_sv_coverage |
steps/calculate_sv_coverage.cwl
(CommandLineTool)
|
||
| normalize_sv_coverage |
steps/normalize_sv_coverage.cwl
(CommandLineTool)
|
||
| postprocess_alignment |
steps/postprocess_alignment.cwl
(CommandLineTool)
|
||
| combine_sample_regions |
steps/combine_sample_regions.cwl
(CommandLineTool)
|
||
| postprocess_alignment_to_rec |
steps/postprocess_alignment_to_rec.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| align_bam | File[] | ||
| sv__calls | f916abb89c0865a73f39c9a1feb3fbc1[] | ||
| variants__gvcf | cebd54c9ce33ab9d6aff7d61800c9841[] | ||
| versions__data | File[] | ||
| variants__calls | ccf12bf1872d2597a3c6631c5e009a98[] | ||
| versions__tools | File[] | ||
| summary__multiqc | File[] | ||
| sv__supplemental | f85a6abcd7f58daaa3d3e47a2ca08fc1[] | ||
| rgnames__sample_out | String[] | ||
| sv__prioritize__raw | 91b64ce598260556aaab74c8bf33dd1e[] | ||
| sv__prioritize__tsv | e37043b8926354c24b294b639e0f5cd7[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] | ||
| svvalidate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
