subworkflows_filter_vcf_nonhuman.cwl
APipe Tester edited this page May 24, 2022
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Apply filters to VCF file
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| vcf | File | |||
| filter_mapq0_threshold | float | |||
| tumor_bam | File | ['.bai'] | ||
| do_cle_vcf_filter | boolean | |||
| filter_somatic_llr_threshold | float | |||
| filter_somatic_llr_tumor_purity | float | |||
| filter_somatic_llr_normal_contamination_rate | float | |||
| filter_minimum_depth | int | |||
| tumor_sample_name | string | |||
| normal_sample_name | string |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| filtered_vcf | File |
| Name | CWL Run |
|---|---|
| filter_vcf_mapq0 | tools/filter_vcf_mapq0.cwl |
| filter_vcf_cle | tools/filter_vcf_cle.cwl |
| filter_vcf_depth | tools/filter_vcf_depth.cwl |
| filter_vcf_somatic_llr | tools/filter_vcf_somatic_llr.cwl |
| set_final_vcf_name | tools/staged_rename.cwl |