merge_vcfs_and_annotate
pipes/WDL/workflows/merge_vcfs_and_annotate.wdl

WORKFLOW merge_vcfs_and_annotate

File Path pipes/WDL/workflows/merge_vcfs_and_annotate.wdl
WDL Version 1.0
Type workflow

Imports

Namespace Path
interhost ../tasks/tasks_interhost.wdl
intrahost ../tasks/tasks_intrahost.wdl

Workflow: merge_vcfs_and_annotate

Merge VCFs emitted by GATK UnifiedGenotyper and annotate with snpEff.

Inputs

Name Type Description Default
reference_fasta File Reference genome, all segments/chromosomes in one fasta file. Headers must be Genbank accessions. -
in_vcfs_gz Array[File] - -
machine_mem_gb Int? - -
snpEffRef Array[String]? - -
emailAddress String? - -
machine_mem_gb Int? - -
4 optional inputs with default values

Outputs

Name Type Expression
merged_vcf_gz File merge_vcfs.merged_vcf_gz
merged_vcf_gz_tbi File merge_vcfs.merged_vcf_gz_tbi
merged_annot_vcf_gz File annotate_vcf.annot_vcf_gz
merged_annot_vcf_gz_tbi File annotate_vcf.annot_vcf_gz_tbi

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS merge_vcfs ↗ → merge_vcfs_gatk

Input Mappings (1)
Input Value
ref_fasta reference_fasta

CALL TASKS annotate_vcf ↗ → annotate_vcf_snpeff

Input Mappings (2)
Input Value
ref_fasta reference_fasta
in_vcf merge_vcfs.merged_vcf_gz

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 2 tasks:
  • merge_vcfs
  • annotate_vcf
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merge_vcfs_and_annotate - WDL Source Code

version 1.0

import "../tasks/tasks_interhost.wdl" as interhost
import "../tasks/tasks_intrahost.wdl" as intrahost

workflow merge_vcfs_and_annotate {
    meta {
        description: "Merge VCFs emitted by GATK UnifiedGenotyper and annotate with snpEff."
    }

    input {
        File reference_fasta
    }

    parameter_meta {
        reference_fasta: {
          description: "Reference genome, all segments/chromosomes in one fasta file. Headers must be Genbank accessions.",
          patterns: ["*.fasta"]
        }
    }

    call interhost.merge_vcfs_gatk as merge_vcfs {
        input:
            ref_fasta = reference_fasta
    }
    call intrahost.annotate_vcf_snpeff as annotate_vcf {
        input:
            ref_fasta = reference_fasta,
            in_vcf    = merge_vcfs.merged_vcf_gz
    }
    output {
        File merged_vcf_gz           = merge_vcfs.merged_vcf_gz
        File merged_vcf_gz_tbi       = merge_vcfs.merged_vcf_gz_tbi
        File merged_annot_vcf_gz     = annotate_vcf.annot_vcf_gz
        File merged_annot_vcf_gz_tbi = annotate_vcf.annot_vcf_gz_tbi
    }
}