kraken2_build - WDL Atlas

WORKFLOW kraken2_build

File Path	`pipes/WDL/workflows/kraken2_build.wdl`
WDL Version	1.0
Type	workflow

Imports

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

Workflow: kraken2_build

Build a Kraken2 (or 2X) database.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`db_basename`	`String`	-	-
`taxonomy_db_tgz`	`File?`	-	-
`kmerLen`	`Int?`	-	-
`minimizerLen`	`Int?`	-	-
`minimizerSpaces`	`Int?`	-	-
`maxDbSize`	`Int?`	-	-
`zstd_compression_level`	`Int?`	-	-
5 optional inputs with default values
`standard_libraries`	`Array[String]`	-	["archaea", "bacteria", "plasmid", "viral", "human", "fungi", "protozoa", "UniVec_Core"]
`custom_libraries`	`Array[File]`	-	[]
`protein`	`Boolean`	-	false
`machine_mem_gb`	`Int`	-	100
`docker`	`String`	-	"quay.io/broadinstitute/viral-classify:2.5.1.0"

Outputs

Name	Type	Expression
`kraken2_db`	`File`	`build_kraken2_db.kraken2_db`
`taxdump_tgz`	`File`	`build_kraken2_db.taxdump_tgz`
`krona_db`	`File`	`build_kraken2_db.krona_db`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `build_kraken2_db` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

build_kraken2_db

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flowchart TD
    Start([kraken2_build])
    N1["build_kraken2_db"]
    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 kraken2_build {
    meta {
        description: "Build a Kraken2 (or 2X) database."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call metagenomics.build_kraken2_db

    output {
        File kraken2_db  = build_kraken2_db.kraken2_db
        File taxdump_tgz = build_kraken2_db.taxdump_tgz
        File krona_db    = build_kraken2_db.krona_db
    }
}