merge_metagenomics
pipes/WDL/workflows/merge_metagenomics.wdl

WORKFLOW merge_metagenomics

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

Imports

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

Workflow: merge_metagenomics

Combine metagenomic reports from single samples into an aggregate report.

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

Inputs

Name Type Description Default
krakenuniq_summary_reports Array[File] - -
krona_per_sample Array[File] - -
6 optional inputs with default values

Outputs

Name Type Expression
krona_merged File krona_merge.krona_report_html
metagenomics_summary File aggregate_metagenomics_reports.krakenuniq_aggregate_taxlevel_summary

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS krona_merge ↗

Input Mappings (2)
Input Value
krona_reports krona_per_sample
out_basename "merged_krona"

CALL TASKS aggregate_metagenomics_reports ↗

Input Mappings (1)
Input Value
kraken_summary_reports krakenuniq_summary_reports

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

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

~{docker}

Used by 1 task:
  • aggregate_metagenomics_reports
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merge_metagenomics - Workflow Graph

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merge_metagenomics - WDL Source Code

version 1.0

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

workflow merge_metagenomics {
    meta {
        description: "Combine metagenomic reports from single samples into an aggregate report."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    input {
        Array[File] krakenuniq_summary_reports
        Array[File] krona_per_sample
    }

    call metagenomics.krona_merge {
        input:
            krona_reports = krona_per_sample,
            out_basename  = "merged_krona"
    }

    call reports.aggregate_metagenomics_reports {
        input:
            kraken_summary_reports = krakenuniq_summary_reports
    }

    output {
        File krona_merged         = krona_merge.krona_report_html
        File metagenomics_summary = aggregate_metagenomics_reports.krakenuniq_aggregate_taxlevel_summary
    }
}