bams_multiqc
pipes/WDL/workflows/bams_multiqc.wdl

WORKFLOW bams_multiqc

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

Imports

Namespace Path
reports ../tasks/tasks_reports.wdl

Workflow: bams_multiqc

Run FastQC on a set of BAM files, and then MultiQC to summarize all outputs.

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

Inputs

Name Type Description Default
read_bams Array[File]+ - -
title String? - -
comment String? - -
file_name String? - -
template String? - -
tag String? - -
ignore_analysis_files String? - -
ignore_sample_names String? - -
sample_names File? - -
exclude_modules Array[String]? - -
module_to_use Array[String]? - -
output_data_format String? - -
config File? - -
config_yaml String? - -
14 optional inputs with default values

Outputs

Name Type Expression
multiqc File MultiQC.multiqc_report
fastqcs Array[File] fastqc.fastqc_html
viral_core_version String fastqc.viralngs_version[0]

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS fastqc ↗

Input Mappings (1)
Input Value
reads_bam reads_bam

CALL TASKS MultiQC ↗

Input Mappings (1)
Input Value
input_files fastqc.fastqc_zip

Images

Container images used by tasks in this workflow:

🐳 ~{docker}

~{docker}

Used by 2 tasks:
  • MultiQC
  • fastqc
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bams_multiqc - Workflow Graph

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bams_multiqc - WDL Source Code

version 1.0

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

workflow bams_multiqc {
    meta {
        description: "Run FastQC on a set of BAM files, and then MultiQC to summarize all outputs."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    input {
        Array[File]+ read_bams
    }

    scatter(reads_bam in read_bams) {
        call reports.fastqc as fastqc {
            input:
                reads_bam = reads_bam
        }
    }

    call reports.MultiQC {
        input:
            input_files = fastqc.fastqc_zip
    }

    output {
        File        multiqc            = MultiQC.multiqc_report
        Array[File] fastqcs            = fastqc.fastqc_html
        String      viral_core_version = fastqc.viralngs_version[0]
    }
}