Workflow: exome alignment and somatic variant detection
Fetched 2023-01-12 06:50:34 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 | ||
| docm_vcf | File | ||
| omni_vcf | File | ||
| dbsnp_vcf | File | ||
| reference | String | ||
| cosmic_vcf | File (Optional) | ||
| tumor_bams | File[] | ||
| normal_bams | File[] | ||
| known_indels | File | ||
| interval_list | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String (Optional) | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| hgvs_annotation | Boolean (Optional) | ||
| varscan_p_value | Float (Optional) | ||
| target_intervals | File | ||
| tumor_readgroups | String[] | ||
| custom_gnomad_vcf | File (Optional) | ||
| normal_readgroups | String[] | ||
| per_base_intervals | File | ||
| pindel_insert_size | Integer | ||
| vep_to_table_fields | String[] | ||
| annotate_coding_only | Boolean (Optional) | ||
| mutect_scatter_count | Integer | ||
| panel_of_normals_vcf | File (Optional) | ||
| per_target_intervals | File | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| varscan_strand_filter | Integer (Optional) | ||
| per_base_bait_intervals | File | ||
| qc_minimum_base_quality | Integer (Optional) | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| per_target_bait_intervals | File | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| mutect_artifact_detection_mode | Boolean | ||
| picard_metric_accumulation_level | String | ||
| variants_to_table_genotype_fields | String[] | ||
| mutect_max_alt_alleles_in_normal_count | Integer (Optional) | ||
| mutect_max_alt_allele_in_normal_fraction | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| detect_variants |
detect_variants/detect_variants.cwl
(Workflow)
|
Detect Variants workflow | |
| tumor_alignment_and_qc |
exome_alignment.cwl
(Workflow)
|
exome alignment with qc | |
| normal_alignment_and_qc |
exome_alignment.cwl
(Workflow)
|
exome alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| vep_summary | File | ||
| tumor_flagstats | File | ||
| normal_flagstats | File | ||
| tumor_hs_metrics | File | ||
| docm_filtered_vcf | File | ||
| normal_hs_metrics | 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 | ||
| tumor_insert_size_metrics | File | ||
| tumor_per_base_hs_metrics | File (Optional) | ||
| tumor_verify_bam_id_depth | File | ||
| normal_insert_size_metrics | File | ||
| normal_per_base_hs_metrics | File (Optional) | ||
| normal_verify_bam_id_depth | File | ||
| tumor_per_target_hs_metrics | File (Optional) | ||
| tumor_verify_bam_id_metrics | File | ||
| normal_per_target_hs_metrics | File (Optional) | ||
| normal_verify_bam_id_metrics | File | ||
| tumor_mark_duplicates_metrics | File | ||
| normal_mark_duplicates_metrics | File | ||
| tumor_alignment_summary_metrics | File | ||
| tumor_per_base_coverage_metrics | File (Optional) | ||
| normal_alignment_summary_metrics | File | ||
| normal_per_base_coverage_metrics | File (Optional) | ||
| tumor_per_target_coverage_metrics | File (Optional) | ||
| normal_per_target_coverage_metrics | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/somatic_exome_workflow.cwl
