Workflow: wgs alignment and tumor-only variant detection
Fetched 2024-10-31 00:53:49 GMT
Verified with cwltool version 3.1.20230201224320
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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 | ||
| docm_vcf | File | ||
| omni_vcf | File | ||
| dbsnp_vcf | File | ||
| reference | String | ||
| readgroups | String[] | ||
| sample_name | String | ||
| known_indels | File | ||
| qc_intervals | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String (Optional) | ||
| custom_gnomad_vcf | File (Optional) | ||
| variant_detection_intervals | File | ||
| readcount_minimum_base_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String | ||
| readcount_minimum_mapping_quality | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| detect_variants |
tumor_only_detect_variants.cwl
(Workflow)
|
Tumor-Only Detect Variants workflow | |
| alignment_and_qc |
wgs_alignment.cwl
(Workflow)
|
wgs alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| final_tsv | File | ||
| final_vcf | File | ||
| flagstats | File | ||
| varscan_vcf | File | ||
| vep_summary | File | ||
| wgs_metrics | File | ||
| annotated_vcf | File | ||
| docm_gatk_vcf | File | ||
| gc_bias_metrics | File | ||
| insert_size_metrics | File | ||
| verify_bam_id_depth | File | ||
| gc_bias_metrics_chart | File | ||
| insert_size_histogram | File | ||
| verify_bam_id_metrics | File | ||
| gc_bias_metrics_summary | File | ||
| mark_duplicates_metrics | File | ||
| tumor_bam_readcount_tsv | File | ||
| alignment_summary_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/641083e9ed933d388f36fa04c00c20a810599e94/definitions/pipelines/wgs.cwl
