trimal - WDL Atlas

WORKFLOW trimal

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

Imports

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

Workflow: trimal

Trim a multiple sequence alignment with Trimal.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`in_aligned_fasta`	`File`	-	-
`machine_mem_gb`	`Int?`	-	-
2 optional inputs with default values
`docker`	`String`	-	"quay.io/biocontainers/trimal:1.4.1--h6bb024c_3"
`input_basename`	`String`	-	basename(basename(in_aligned_fasta,".fasta"),".fa")

Outputs

Name	Type	Expression
`trimmed_alignment`	`File`	`trimal_clean_msa.trimal_cleaned_fasta`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `trimal_clean_msa` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

trimal_clean_msa

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flowchart TD
    Start([trimal])
    N1["trimal_clean_msa"]
    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 trimal {
    meta {
        description: "Trim a multiple sequence alignment with Trimal."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call interhost.trimal_clean_msa

    output {
        File trimmed_alignment = trimal_clean_msa.trimal_cleaned_fasta
    }
}