Workflow: exome alignment and germline variant detection, with optitype for HLA typing
Fetched 2023-01-05 05:00:02 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 |
|---|---|---|---|
| mills | File | ||
| omni_vcf | File | ||
| sequence | https://w3id.org/cwl/view/git/6b365b79675b2aabfb8d5829bb8df0a6e986b037/definitions/types/sequence_data.yml#sequence_data[] | ||
| dbsnp_vcf | File | ||
| intervals | aec683a8cbc501195d62c1277116d83c[] | ||
| reference | String | ||
| known_indels | File | ||
| gvcf_gq_bands | String[] | ||
| optitype_name | String (Optional) | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] (Optional) | ||
| target_intervals | File | ||
| custom_gnomad_vcf | File (Optional) | ||
| summary_intervals | https://w3id.org/cwl/view/git/6b365b79675b2aabfb8d5829bb8df0a6e986b037/definitions/types/labelled_file.yml#labelled_file[] | ||
| custom_clinvar_vcf | File (Optional) | ||
| per_base_intervals | https://w3id.org/cwl/view/git/6b365b79675b2aabfb8d5829bb8df0a6e986b037/definitions/types/labelled_file.yml#labelled_file[] | ||
| vep_ensembl_species | String |
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
|
| vep_ensembl_version | String |
ensembl version - Must be present in the cache directory. Example: 95 |
|
| annotate_coding_only | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/6b365b79675b2aabfb8d5829bb8df0a6e986b037/definitions/types/labelled_file.yml#labelled_file[] | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| emit_reference_confidence | String | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| optitype |
../tools/optitype_dna.cwl
(CommandLineTool)
|
Run optitype on dna samples | |
| germline_exome |
germline_exome.cwl
(Workflow)
|
exome alignment and germline variant detection |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| gvcf | File[] | ||
| final_vcf | File | ||
| flagstats | File | ||
| coding_vcf | File | ||
| hs_metrics | File | ||
| limited_vcf | File | ||
| vep_summary | File | ||
| optitype_tsv | File | ||
| optitype_plot | File | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File[] | ||
| verify_bam_id_depth | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| verify_bam_id_metrics | File | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/6b365b79675b2aabfb8d5829bb8df0a6e986b037/definitions/pipelines/germline_exome_hla_typing.cwl
