classify_kaiju - WDL Atlas

WORKFLOW classify_kaiju

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

Imports

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

Workflow: classify_kaiju

Taxonomic classification of reads with kaiju.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`reads_unmapped_bam`	`File`	-	-
`kaiju_db_lz4`	`File`	-	-
`ncbi_taxonomy_db_tgz`	`File`	-	-
`krona_taxonomy_db_tgz`	`File`	-	-
2 optional inputs with default values
`machine_mem_gb`	`Int`	-	100
`docker`	`String`	-	"quay.io/broadinstitute/viral-classify:2.5.1.0"

Outputs

Name	Type	Expression
`kaiju_report`	`File`	`kaiju.kaiju_report`
`kaiju_reads`	`File`	`kaiju.kaiju_reads`
`krona_report_html`	`File`	`kaiju.krona_report_html`
`viral_classify_version`	`String`	`kaiju.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `kaiju` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

kaiju

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flowchart TD
    Start([classify_kaiju])
    N1["kaiju"]
    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_kaiju {
    meta {
        description: "Taxonomic classification of reads with kaiju."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call metagenomics.kaiju
    output {
        File   kaiju_report           = kaiju.kaiju_report
        File   kaiju_reads            = kaiju.kaiju_reads
        File   krona_report_html      = kaiju.krona_report_html
        String viral_classify_version = kaiju.viralngs_version
    }
}