- 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 | 73dd26bf3dfcbd96a242950229b0b0e7[] | ||
reference | String | ||
readgroups | String[] | ||
known_indels | File | ||
gvcf_gq_bands | String[] | ||
synonyms_file | File (Optional) | ||
vep_cache_dir | String (Optional) | ||
bait_intervals | File | ||
bqsr_intervals | String[] (Optional) | ||
hgvs_annotation | Boolean (Optional) | ||
target_intervals | File | ||
custom_gnomad_vcf | File (Optional) | ||
per_base_intervals | File | ||
annotate_coding_only | Boolean (Optional) | ||
per_target_intervals | File | ||
per_base_bait_intervals | File | ||
qc_minimum_base_quality | Integer (Optional) | ||
emit_reference_confidence | String | ||
per_target_bait_intervals | File | ||
qc_minimum_mapping_quality | Integer (Optional) | ||
picard_metric_accumulation_level | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
detect_variants |
detect_variants/germline_detect_variants.cwl
(Workflow)
|
exome alignment and germline variant detection | |
extract_freemix |
germline_exome_workflow.cwl#extract_freemix/76a74fe6-d89d-4903-876b-91327651b883
(ExpressionTool)
|
||
alignment_and_qc |
exome_alignment.cwl
(Workflow)
|
exome alignment with qc |
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 | ||
insert_size_metrics | File | ||
per_base_hs_metrics | File (Optional) | ||
verify_bam_id_depth | File | ||
insert_size_histogram | File | ||
per_target_hs_metrics | File (Optional) | ||
verify_bam_id_metrics | File | ||
mark_duplicates_metrics | File | ||
alignment_summary_metrics | File | ||
per_base_coverage_metrics | File (Optional) | ||
per_target_coverage_metrics | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/germline_exome_workflow.cwl