merge_vcfs - WDL Atlas

WORKFLOW merge_vcfs

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

Imports

Namespace	Path
`interhost`	`../tasks/tasks_interhost.wdl`

Workflow: merge_vcfs

Merge VCFs from multiple samples using GATK3.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`in_vcfs_gz`	`Array[File]`	-	-
`ref_fasta`	`File`	-	-
`machine_mem_gb`	`Int?`	-	-
2 optional inputs with default values
`docker`	`String`	-	"quay.io/broadinstitute/viral-phylo:2.5.1.0"
`output_prefix`	`String`	-	"merged"

Outputs

Name	Type	Expression
`merged_vcf_gz`	`File`	`merge_vcfs_gatk.merged_vcf_gz`
`merged_vcf_gz_tbi`	`File`	`merge_vcfs_gatk.merged_vcf_gz_tbi`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `merge_vcfs_gatk` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

merge_vcfs_gatk

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flowchart TD
    Start([merge_vcfs])
    N1["merge_vcfs_gatk"]
    Start --> N1
    N1 --> End([End])
    classDef taskNode fill:#a371f7,stroke:#8b5cf6,stroke-width:2px,color:#fff
    classDef workflowNode fill:#58a6ff,stroke:#1f6feb,stroke-width:2px,color:#fff

version 1.0

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

workflow merge_vcfs {
    meta {
        description: "Merge VCFs from multiple samples using GATK3."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }
    call interhost.merge_vcfs_gatk
    output {
        File merged_vcf_gz     = merge_vcfs_gatk.merged_vcf_gz
        File merged_vcf_gz_tbi = merge_vcfs_gatk.merged_vcf_gz_tbi
    }
}