downsample - WDL Atlas

WORKFLOW downsample

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

Imports

Namespace	Path
`reads`	`../tasks/tasks_read_utils.wdl`

Workflow: downsample

Random subsampling of reads.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`reads_bam`	`Array[File]+`	-	-
`readCount`	`Int?`	-	-
`machine_mem_gb`	`Int?`	-	-
3 optional inputs with default values
`deduplicateBefore`	`Boolean`	-	false
`deduplicateAfter`	`Boolean`	-	false
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"

Outputs

Name	Type	Expression
`downsampled_bam`	`Array[File]`	`downsample_bams.downsampled_bam`
`viralngs_version`	`String`	`downsample_bams.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `downsample_bams` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

downsample_bams

← Back to Index

flowchart TD
    Start([downsample])
    N1["downsample_bams"]
    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_read_utils.wdl" as reads

workflow downsample {
    meta {
        description: "Random subsampling of reads."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call reads.downsample_bams

    output {
      Array[File] downsampled_bam  = downsample_bams.downsampled_bam
      String      viralngs_version = downsample_bams.viralngs_version
    }
}