isnvs_lofreq - WDL Atlas

WORKFLOW isnvs_lofreq

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

Imports

Namespace	Path
`intrahost`	`../tasks/tasks_intrahost.wdl`

Workflow: isnvs_lofreq

variant calls by LoFreq against reference_fasta

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`aligned_bams`	`Array[File]+`	reads aligned to the sequence within reference_fasta.	-
`reference_fasta`	`File`	Reference sequence to which reads have be aligned	-
2 optional inputs with default values
`out_basename`	`String`	-	basename(aligned_bam,'.bam')
`docker`	`String`	-	"quay.io/broadinstitute/viral-phylo:2.5.1.0"

Outputs

Name	Type	Expression
`lofreq_vcfs`	`Array[File]`	`lofreq.report_vcf`
`lofreq_version`	`String`	`lofreq.lofreq_version[0]`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `lofreq` ↗

Input Mappings (2)

Input	Value
`aligned_bam`	`aligned_bam`
`reference_fasta`	`reference_fasta`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

lofreq

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flowchart TD
    Start([isnvs_lofreq])
    subgraph S1 ["🔃 scatter aligned_bam in aligned_bams"]
        direction TB
        N1["lofreq"]
    end
    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_intrahost.wdl" as intrahost

workflow isnvs_lofreq {
    meta {
        description: "variant calls by LoFreq against reference_fasta"
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    parameter_meta {
        aligned_bams: {
            description: "reads aligned to the sequence within reference_fasta.",
            patterns: ["*.bam"]
        }
        reference_fasta: {
            description: "Reference sequence to which reads have be aligned",
            patterns: ["*.fasta"]
        }
    }

    input {
        Array[File]+ aligned_bams
        File         reference_fasta
    }

    scatter(aligned_bam in aligned_bams) {
        call intrahost.lofreq as lofreq {
            input:
                aligned_bam = aligned_bam,
                reference_fasta = reference_fasta
        }
    }

    output {
        Array[File] lofreq_vcfs           = lofreq.report_vcf
        String      lofreq_version        = lofreq.lofreq_version[0]
    }
}