qiime_import_bam - WDL Atlas

WORKFLOW qiime_import_bam

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

Imports

Namespace	Path
`infile`	`../tasks/tasks_16S_amplicon.wdl`

Workflow: qiime_import_bam

Importing BAM files into QIIME

Author: fnegrete

viral_ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`reads_bam`	`Array[File]`	-	-
4 optional inputs with default values
`memory_mb`	`Int`	-	7000
`cpu`	`Int`	-	5
`disk_size_gb`	`Int`	-	ceil((2 * 20)) + 5
`docker`	`String`	-	"quay.io/broadinstitute/qiime2:latest"

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `qiime_import_from_bam` ↗

Input Mappings (1)

Input	Value
`reads_bam`	`reads_bam`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

qiime_import_from_bam

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flowchart TD
    Start([qiime_import_bam])
    N1["qiime_import_from_bam"]
    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

#DX_SKIP_WORKFLOW

import "../tasks/tasks_16S_amplicon.wdl" as infile

workflow qiime_import_bam {
    
meta{
    description: "Importing BAM files into QIIME"
    author: "fnegrete"
    email:  "viral_ngs@broadinstitute.org"
    allowNestedInputs: true 
}
input {
    Array[File]    reads_bam
}

call infile.qiime_import_from_bam {
    input: 
            reads_bam  = reads_bam
    }
}