Workflow: Detect Variants workflow
Fetched 2024-04-26 19:08:43 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 |
|---|---|---|---|
| docm_vcf | File | ||
| dbsnp_vcf | File (Optional) | ||
| reference | String | ||
| cosmic_vcf | File (Optional) | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| interval_list | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String (Optional) | ||
| cle_vcf_filter | Boolean (Optional) | ||
| hgvs_annotation | Boolean (Optional) | ||
| varscan_p_value | Float (Optional) | ||
| custom_gnomad_vcf | File (Optional) | ||
| pindel_insert_size | Integer | ||
| strelka_exome_mode | Boolean | ||
| vep_to_table_fields | String[] (Optional) | ||
| annotate_coding_only | Boolean (Optional) | ||
| mutect_scatter_count | Integer (Optional) | ||
| panel_of_normals_vcf | File (Optional) | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| varscan_strand_filter | Integer (Optional) | ||
| filter_mapq0_threshold | Float (Optional) | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] (Optional) | ||
| mutect_artifact_detection_mode | Boolean (Optional) | ||
| readcount_minimum_base_quality | Integer (Optional) | ||
| readcount_minimum_mapping_quality | Integer (Optional) | ||
| variants_to_table_genotype_fields | String[] (Optional) | ||
| mutect_max_alt_alleles_in_normal_count | Integer (Optional) | ||
| mutect_max_alt_allele_in_normal_fraction | Float (Optional) | ||
| filter_gnomADe_maximum_population_allele_frequency | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| docm |
../docm/workflow.cwl
(Workflow)
|
Detect Docm variants | |
| index |
index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| mutect |
../mutect/workflow.cwl
(Workflow)
|
mutect parallel workflow | |
| pindel |
../pindel/workflow.cwl
(Workflow)
|
pindel parallel workflow | |
| combine |
combine_variants.cwl
(CommandLineTool)
|
CombineVariants (GATK 3.6) | |
| strelka |
../strelka/workflow.cwl
(Workflow)
|
strelka workflow | |
| varscan |
../varscan/workflow.cwl
(Workflow)
|
Varscan Workflow | |
| filter_vcf |
filter_vcf.cwl
(Workflow)
|
Apply filters to VCF file | |
| annotate_variants |
vep.cwl
(CommandLineTool)
|
Ensembl Variant Effect Predictor | |
| tumor_cram_to_bam |
../cram_to_bam/workflow.cwl
(Workflow)
|
cram_to_bam workflow | |
| variants_to_table |
variants_to_table.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
| normal_cram_to_bam |
../cram_to_bam/workflow.cwl
(Workflow)
|
cram_to_bam workflow | |
| tumor_bam_readcount |
../pvacseq/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| normal_bam_readcount |
../pvacseq/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| annotated_filter_bgzip |
bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| annotated_filter_index |
index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| add_vep_fields_to_table |
add_vep_fields_to_table.cwl
(CommandLineTool)
|
add VEP annotation to report | |
| add_tumor_bam_readcount_to_vcf |
add_bam_readcount_to_vcf.cwl
(CommandLineTool)
|
add bam_readcount info to vcf | |
| add_normal_bam_readcount_to_vcf |
add_bam_readcount_to_vcf.cwl
(CommandLineTool)
|
add bam_readcount info to vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| vep_summary | File | ||
| docm_filtered_vcf | File | ||
| final_filtered_vcf | File | ||
| docm_unfiltered_vcf | File | ||
| mutect_filtered_vcf | File | ||
| pindel_filtered_vcf | File | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| pindel_unfiltered_vcf | File | ||
| strelka_unfiltered_vcf | File | ||
| varscan_unfiltered_vcf | File | ||
| tumor_bam_readcount_tsv | File | ||
| normal_bam_readcount_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/detect_variants/detect_variants.cwl
