multiqc_only - WDL Atlas

WORKFLOW multiqc_only

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

Imports

Namespace	Path
`reports`	`../tasks/tasks_reports.wdl`

Workflow: multiqc_only

Combine multiple FastQC reports into a single MultiQC summary.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`input_files`	`Array[File]`	-	-
`title`	`String?`	-	-
`comment`	`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
`file_name`	`String`	-	"multiqc-raw.html"
`out_dir`	`String`	-	"./multiqc-output"
`force`	`Boolean`	-	false
`full_names`	`Boolean`	-	false
`data_dir`	`Boolean`	-	false
`no_data_dir`	`Boolean`	-	false
`zip_data_dir`	`Boolean`	-	false
`export`	`Boolean`	-	false
`flat`	`Boolean`	-	false
`interactive`	`Boolean`	-	true
`lint`	`Boolean`	-	false
`pdf`	`Boolean`	-	false
`megaQC_upload`	`Boolean`	-	false
`docker`	`String`	-	"quay.io/biocontainers/multiqc:1.32--pyhdfd78af_1"

Outputs

Name	Type	Expression
`multiqc`	`File`	`MultiQC.multiqc_report`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `MultiQC` ↗

Input Mappings (2)

Input	Value
`input_files`	`input_files`
`file_name`	`file_name`

Images

Container images used by tasks in this workflow:

🐳 ~{docker}

~{docker}

Used by 1 task:

MultiQC

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flowchart TD
    Start([multiqc_only])
    N1["MultiQC"]
    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_reports.wdl" as reports

workflow multiqc_only {
    meta {
        description: "Combine multiple FastQC reports into a single MultiQC summary."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }
    input {
        Array[File] input_files
        String      file_name = "multiqc-raw.html"
    }
    call reports.MultiQC {
        input:
            input_files = input_files,
            file_name = file_name
    }
    output {
        File multiqc = MultiQC.multiqc_report
    }
}