Workflow: exome alignment and germline variant detection
Fetched 2025-09-15 17:29:23 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| bams | File[] | ||
| mills | File | ||
| omni_vcf | File | ||
| dbsnp_vcf | File | ||
| intervals | f5e65c4b1cbba6338e1d5f4eec61b032[] | ||
| reference | String | ||
| readgroups | String[] | ||
| vep_plugins | String[] (Optional) |
array of plugins to use when running vep |
|
| known_indels | File | ||
| gvcf_gq_bands | String[] | ||
| 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/7f9dfad8e45ca096ae738cff646195b2b1ba7d7f/definitions/types/labelled_file.yml#labelled_file[] | ||
| custom_clinvar_vcf | File (Optional) | ||
| per_base_intervals | https://w3id.org/cwl/view/git/7f9dfad8e45ca096ae738cff646195b2b1ba7d7f/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 |
|
| vep_to_table_fields | String[] (Optional) | ||
| annotate_coding_only | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/7f9dfad8e45ca096ae738cff646195b2b1ba7d7f/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) | ||
| variants_to_table_fields | String[] (Optional) | ||
| emit_reference_confidence | String | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String | ||
| variants_to_table_genotype_fields | String[] (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| detect_variants |
../subworkflows/germline_detect_variants.cwl
(Workflow)
|
exome alignment and germline variant detection | |
| extract_freemix |
germline_exome.cwl#extract_freemix/1902dd5d-bc3d-4145-88d0-754c8bbed6df
(ExpressionTool)
|
||
| alignment_and_qc |
exome_alignment.cwl
(Workflow)
|
exome alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| gvcf | File[] | ||
| final_tsv | File | ||
| final_vcf | File | ||
| flagstats | File | ||
| coding_vcf | File | ||
| hs_metrics | File | ||
| limited_vcf | File | ||
| vep_summary | 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/7f9dfad8e45ca096ae738cff646195b2b1ba7d7f/definitions/pipelines/germline_exome.cwl
