isnvs_one_sample - WDL Atlas

WORKFLOW isnvs_one_sample

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

Imports

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

Workflow: isnvs_one_sample

Intrahost variant calling with V-Phaser2. Requires an assembled genome and a BAM of aligned reads against that same genome.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`mapped_bam`	`File`	-	-
`assembly_fasta`	`File`	-	-
`threads`	`Int?`	-	-
`minReadsPerStrand`	`Int?`	-	-
`maxBias`	`Int?`	-	-
`machine_mem_gb`	`Int?`	-	-
3 optional inputs with default values
`removeDoublyMappedReads`	`Boolean`	-	true
`docker`	`String`	-	"quay.io/broadinstitute/viral-phylo:2.5.1.0"
`sample_name`	`String`	-	basename(basename(basename(mapped_bam,".bam"),".all"),".mapped")

Outputs

Name	Type	Expression
`isnvsFile`	`File`	`isnvs_per_sample.isnvsFile`
`isnvs_viral_phylo_version`	`String`	`isnvs_per_sample.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `isnvs_per_sample` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 ~{docker}

~{docker}

Used by 1 task:

isnvs_per_sample

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flowchart TD
    Start([isnvs_one_sample])
    N1["isnvs_per_sample"]
    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_one_sample {
    meta {
        description: "Intrahost variant calling with V-Phaser2. Requires an assembled genome and a BAM of aligned reads against that same genome."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call intrahost.isnvs_per_sample

    output {
        File   isnvsFile                 = isnvs_per_sample.isnvsFile
        String isnvs_viral_phylo_version = isnvs_per_sample.viralngs_version
    }
}