- 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 |
---|---|---|---|
bam | File | ||
ploidy | Integer (Optional) | ||
intervals | 28de077b27b118c3e6377200012d74de[] | ||
reference | File | ||
vep_plugins | String[] | ||
gvcf_gq_bands | String[] | ||
synonyms_file | File (Optional) | ||
vep_cache_dir | Directory | ||
final_tsv_prefix | String (Optional) | ||
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) | ||
vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
contamination_fraction | String (Optional) | ||
vep_custom_annotations | https://w3id.org/cwl/view/git/700e73aaed6db1ad538dd27b2e1709f436ad3edb/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
limit_variant_intervals | File | ||
variants_to_table_fields | String[] (Optional) | ||
emit_reference_confidence | |||
variants_to_table_genotype_fields | String[] (Optional) | ||
filter_gnomAD_maximum_population_allele_frequency | Float |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
filter_vcf |
germline_filter_vcf.cwl
(Workflow)
|
Apply filters to VCF file | |
genotype_gvcfs |
../tools/gatk_genotypegvcfs.cwl
(CommandLineTool)
|
GATK HaplotypeCaller | |
haplotype_caller |
gatk_haplotypecaller_iterator.cwl
(Workflow)
|
scatter GATK HaplotypeCaller over intervals | |
annotate_variants |
../tools/vep.cwl
(CommandLineTool)
|
Ensembl Variant Effect Predictor | |
set_final_tsv_name |
../tools/staged_rename.cwl
(CommandLineTool)
|
Staged Renamer |
Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead. |
bgzip_annotated_vcf |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
index_annotated_vcf |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
set_filtered_tsv_name |
../tools/staged_rename.cwl
(CommandLineTool)
|
Staged Renamer |
Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead. |
final_variants_to_table |
../tools/variants_to_table.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
filtered_variants_to_table |
../tools/variants_to_table.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
final_add_vep_fields_to_table |
../tools/add_vep_fields_to_table.cwl
(CommandLineTool)
|
add VEP annotation to report | |
filtered_add_vep_fields_to_table |
../tools/add_vep_fields_to_table.cwl
(CommandLineTool)
|
add VEP annotation to report |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
gvcf | File[] | ||
final_tsv | File | ||
final_vcf | File | ||
vep_summary | File | ||
filtered_tsv | File | ||
filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/700e73aaed6db1ad538dd27b2e1709f436ad3edb/definitions/subworkflows/germline_detect_variants.cwl