coverage_table - WDL Atlas

WORKFLOW coverage_table

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

Imports

Namespace	Path
`reports`	`../tasks/tasks_reports.wdl`

Workflow: coverage_table

Inputs

Name	Type	Description	Default
`mapped_bams`	`Array[File]+`	-	-
3 optional inputs with default values
`mapped_bam_idx`	`Array[File]`	-	[]
`out_report_name`	`String`	-	"coverage_report.txt"
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"

Outputs

Name	Type	Expression
`coverage_report_txt`	`File`	`coverage_report.coverage_report`
`viral_core_version`	`String`	`coverage_report.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `coverage_report` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

coverage_report

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flowchart TD
    Start([coverage_table])
    N1["coverage_report"]
    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_reports.wdl" as reports

workflow coverage_table {
    call reports.coverage_report
    output {
        File   coverage_report_txt = coverage_report.coverage_report
        String viral_core_version  = coverage_report.viralngs_version
    }
}