mafft_and_trim
pipes/WDL/workflows/mafft_and_trim.wdl

WORKFLOW mafft_and_trim

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

Imports

Namespace Path
interhost ../tasks/tasks_interhost.wdl

Workflow: mafft_and_trim

MAFFT based multiple alignment followed by trimal-based edge trimming.

Author: Broad Viral Genomics
viral-ngs@broadinstitute.org

Inputs

Name Type Description Default
assemblies_fasta Array[File]+ - -
mafft_maxIters Int? - -
mafft_ep Float? - -
mafft_gapOpeningPenalty Float? - -
machine_mem_gb Int? - -
machine_mem_gb Int? - -
4 optional inputs with default values

Outputs

Name Type Expression
alignments_by_chr Array[File] mafft.alignments_by_chr
trimmed_alignements_by_chr Array[File] trimal.trimal_cleaned_fasta
sampleNamesFile File mafft.sampleNamesFile
viral_phylo_version String mafft.viralngs_version

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS mafft ↗ → multi_align_mafft

No explicit input mappings

CALL TASKS trimal ↗ → trimal_clean_msa

Input Mappings (1)
Input Value
in_aligned_fasta alignment

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • mafft
🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • trimal
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mafft_and_trim - Workflow Graph

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mafft_and_trim - WDL Source Code

version 1.0

import "../tasks/tasks_interhost.wdl" as interhost

workflow mafft_and_trim {
    meta {
        description: "MAFFT based multiple alignment followed by trimal-based edge trimming."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call interhost.multi_align_mafft as mafft

    scatter(alignment in mafft.alignments_by_chr) {
        call interhost.trimal_clean_msa as trimal {
            input:
                in_aligned_fasta = alignment
        }
    }

    output {
        Array[File] alignments_by_chr          = mafft.alignments_by_chr
        Array[File] trimmed_alignements_by_chr = trimal.trimal_cleaned_fasta
        File        sampleNamesFile            = mafft.sampleNamesFile
        String      viral_phylo_version        = mafft.viralngs_version
    }
}