mafft - WDL Atlas

WORKFLOW mafft

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

Imports

Namespace	Path
`interhost`	`../tasks/tasks_interhost.wdl`

Workflow: mafft

MAFFT multiple-alignment for a set of possibly multi-segment genomes.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`reference_fasta`	`File`	-	-
`assemblies_fasta`	`Array[File]+`	-	-
`mafft_maxIters`	`Int?`	-	-
`mafft_ep`	`Float?`	-	-
`mafft_gapOpeningPenalty`	`Float?`	-	-
`machine_mem_gb`	`Int?`	-	-
1 optional input with default value
`docker`	`String`	-	"quay.io/broadinstitute/viral-phylo:2.5.1.0"

Outputs

Name	Type	Expression
`alignments_by_chr`	`Array[File]`	`multi_align_mafft_ref.alignments_by_chr`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `multi_align_mafft_ref` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

multi_align_mafft_ref

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flowchart TD
    Start([mafft])
    N1["multi_align_mafft_ref"]
    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_interhost.wdl" as interhost

workflow mafft {
    meta {
        description: "MAFFT multiple-alignment for a set of possibly multi-segment genomes."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call interhost.multi_align_mafft_ref

    output {
        #File        sampleNamesFile     = multi_align_mafft_ref.sampleNamesFile
        Array[File] alignments_by_chr   = multi_align_mafft_ref.alignments_by_chr
    }
}