classify_krakenuniq
pipes/WDL/workflows/classify_krakenuniq.wdl

WORKFLOW classify_krakenuniq

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

Imports

Namespace Path
metagenomics ../tasks/tasks_metagenomics.wdl
reports ../tasks/tasks_reports.wdl

Workflow: classify_krakenuniq

Taxonomic classification of reads using krakenuniq v1.

Author: Broad Viral Genomics
viral-ngs@broadinstitute.org

Inputs

Name Type Description Default
reads_unmapped_bam Array[File] - -
krakenuniq_db_tar_lz4 File - -
krona_taxonomy_db_tgz File - -
6 optional inputs with default values

Outputs

Name Type Expression
krakenuniq_krona_merged File krakenuniq.krona_report_merged_html
metagenomics_summary File metag_summary_report.krakenuniq_aggregate_taxlevel_summary
krakenuniq_classified_reads Array[File] krakenuniq.krakenuniq_classified_reads
krakenuniq_summary_reports Array[File] krakenuniq.krakenuniq_summary_reports
krakenuniq_krona_by_sample Array[File] krakenuniq.krona_report_html
viral_classify_version String krakenuniq.viralngs_version

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS krakenuniq ↗

No explicit input mappings

CALL TASKS metag_summary_report ↗ → aggregate_metagenomics_reports

Input Mappings (1)
Input Value
kraken_summary_reports krakenuniq.krakenuniq_summary_reports

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • krakenuniq
🐳 ~{docker}

~{docker}

Used by 1 task:
  • metag_summary_report
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classify_krakenuniq - Workflow Graph

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classify_krakenuniq - WDL Source Code

version 1.0

import "../tasks/tasks_metagenomics.wdl" as metagenomics
import "../tasks/tasks_reports.wdl" as reports

workflow classify_krakenuniq {
    meta {
        description: "Taxonomic classification of reads using krakenuniq v1."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call metagenomics.krakenuniq

    call reports.aggregate_metagenomics_reports as metag_summary_report {
        input:
            kraken_summary_reports = krakenuniq.krakenuniq_summary_reports
    }

    output {
        File        krakenuniq_krona_merged     = krakenuniq.krona_report_merged_html
        File        metagenomics_summary        = metag_summary_report.krakenuniq_aggregate_taxlevel_summary
        Array[File] krakenuniq_classified_reads = krakenuniq.krakenuniq_classified_reads
        Array[File] krakenuniq_summary_reports  = krakenuniq.krakenuniq_summary_reports
        Array[File] krakenuniq_krona_by_sample  = krakenuniq.krona_report_html
        String      viral_classify_version      = krakenuniq.viralngs_version
    }
}