isnvs_merge_to_vcf
pipes/WDL/workflows/isnvs_merge_to_vcf.wdl

WORKFLOW isnvs_merge_to_vcf

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

Imports

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

Workflow: isnvs_merge_to_vcf

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? - -
vphaser2Calls Array[File] - -
snpEffRef Array[String]? - -
sampleNames Array[String]? - -
emailAddress String? - -
machine_mem_gb Int? - -
3 optional inputs with default values

Outputs

Name Type Expression
alignments_by_chr Array[File] mafft.alignments_by_chr
isnvs_plain_vcf File isnvs_vcf.isnvs_vcf
isnvs_plain_vcf_idx File isnvs_vcf.isnvs_vcf_idx
isnvs_annot_vcf File isnvs_vcf.isnvs_annot_vcf
isnvs_annot_vcf_idx File isnvs_vcf.isnvs_annot_vcf_idx
isnvs_annot_txt File isnvs_vcf.isnvs_annot_txt
viral_phylo_version String mafft.viralngs_version

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS mafft ↗ → multi_align_mafft_ref

Input Mappings (2)
Input Value
reference_fasta reference_fasta
assemblies_fasta assemblies_fasta

CALL TASKS isnvs_vcf ↗

Input Mappings (2)
Input Value
perSegmentMultiAlignments mafft.alignments_by_chr
reference_fasta reference_fasta

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • mafft
🐳 ~{docker}

~{docker}

Used by 1 task:
  • isnvs_vcf
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isnvs_merge_to_vcf - Workflow Graph

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isnvs_merge_to_vcf - WDL Source Code

version 1.0

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

workflow isnvs_merge_to_vcf {
    input {
        File          reference_fasta
        Array[File]+  assemblies_fasta     # one per genome
    }

    call interhost.multi_align_mafft_ref as mafft {
        input:
            reference_fasta  = reference_fasta,
            assemblies_fasta = assemblies_fasta
    }

    call tasks_intrahost.isnvs_vcf {
        input:
            perSegmentMultiAlignments = mafft.alignments_by_chr,
            reference_fasta           = reference_fasta
    }

    output {
        Array[File] alignments_by_chr   = mafft.alignments_by_chr
        File        isnvs_plain_vcf     = isnvs_vcf.isnvs_vcf
        File        isnvs_plain_vcf_idx = isnvs_vcf.isnvs_vcf_idx
        File        isnvs_annot_vcf     = isnvs_vcf.isnvs_annot_vcf
        File        isnvs_annot_vcf_idx = isnvs_vcf.isnvs_annot_vcf_idx
        File        isnvs_annot_txt     = isnvs_vcf.isnvs_annot_txt
        String      viral_phylo_version = mafft.viralngs_version
    }
}