classify_kraken2 - WDL Atlas

WORKFLOW classify_kraken2

File Path	`pipes/WDL/workflows/classify_kraken2.wdl`
WDL Version	1.0
Type	workflow

Imports

Namespace	Path
`metagenomics`	`../tasks/tasks_metagenomics.wdl`

Workflow: classify_kraken2

Taxonomic classification of sequences via kraken2 (or kraken2x, depending on the database provided).

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`reads_bam`	`File`	-	-
`kraken2_db_tgz`	`File`	-	-
`krona_taxonomy_db_tgz`	`File`	-	-
`min_base_qual`	`Int?`	-	-
3 optional inputs with default values
`confidence_threshold`	`Float?`	-	0.05
`machine_mem_gb`	`Int`	-	90
`docker`	`String`	-	"quay.io/broadinstitute/viral-classify:2.5.1.0"

Outputs

Name	Type	Expression
`kraken2_reads_report`	`File`	`kraken2.kraken2_reads_report`
`kraken2_summary_report`	`File`	`kraken2.kraken2_summary_report`
`krona_report_html`	`File`	`kraken2.krona_report_html`
`viral_classify_version`	`String`	`kraken2.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `kraken2` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

kraken2

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flowchart TD
    Start([classify_kraken2])
    N1["kraken2"]
    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_metagenomics.wdl" as metagenomics

workflow classify_kraken2 {
    meta {
        description: "Taxonomic classification of sequences via kraken2 (or kraken2x, depending on the database provided)."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }

    call metagenomics.kraken2

    output {
        File   kraken2_reads_report   = kraken2.kraken2_reads_report
        File   kraken2_summary_report = kraken2.kraken2_summary_report
        File   krona_report_html      = kraken2.krona_report_html
        String viral_classify_version = kraken2.viralngs_version
    }
}