merge_bams - WDL Atlas

WORKFLOW merge_bams

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

Imports

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

Workflow: merge_bams

Merge, reheader, or merge-and-reheader BAM files.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`in_bams`	`Array[File]+`	-	-
`sample_name`	`String?`	-	-
`reheader_table`	`File?`	-	-
5 optional inputs with default values
`out_basename`	`String`	-	basename(in_bams[0],".bam")
`run_fastqc`	`Boolean`	-	false
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`disk_size`	`Int`	-	750
`machine_mem_gb`	`Int`	-	4

Outputs

Name	Type	Expression
`out_bam`	`File`	`merge_and_reheader_bams.out_bam`
`viral_core_version`	`String`	`merge_and_reheader_bams.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `merge_and_reheader_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:

merge_and_reheader_bams

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flowchart TD
    Start([merge_bams])
    N1["merge_and_reheader_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 read_utils

workflow merge_bams {
    meta {
        description: "Merge, reheader, or merge-and-reheader BAM files."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call read_utils.merge_and_reheader_bams
    output {
        File   out_bam            = merge_and_reheader_bams.out_bam
        String viral_core_version = merge_and_reheader_bams.viralngs_version
    }   
}