calc_bam_read_depths

WORKFLOW calc_bam_read_depths

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

Imports

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

Workflow: calc_bam_read_depths

Generates read depth tables.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`aligned_bams`	`Array[File]+`	Reads aligned to a reference sequence.	-
2 optional inputs with default values
`out_basename`	`String`	-	basename(aligned_bam,'.bam')
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"

Outputs

Name	Type	Expression
`read_depths`	`Array[File]`	`depth.read_depths`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `depth` ↗ → read_depths

Input Mappings (1)

Input	Value
`aligned_bam`	`aligned_bam`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

depth

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flowchart TD
    Start([calc_bam_read_depths])
    subgraph S1 ["🔃 scatter aligned_bam in aligned_bams"]
        direction TB
        N1["depth
read_depths"]
    end
    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 read_utils

workflow calc_bam_read_depths {
    meta {
        description: "Generates read depth tables."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    parameter_meta {
        aligned_bams: {
            description: "Reads aligned to a reference sequence.",
            patterns: ["*.bam"]
        }
    }

    input {
        Array[File]+ aligned_bams
    }

    scatter(aligned_bam in aligned_bams) {
        
        call read_utils.read_depths as depth {
            input:
                aligned_bam = aligned_bam
        }
    }

    output {
        Array[File] read_depths = depth.read_depths
    }
}