fastq_to_ubam - WDL Atlas

WORKFLOW fastq_to_ubam

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

Imports

Namespace	Path
`tasks_read_utils`	`../tasks/tasks_read_utils.wdl`

Workflow: fastq_to_ubam

Convert reads from fastq format (single or paired) to unaligned BAM format.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`fastq_1`	`File`	-	-
`fastq_2`	`File?`	-	-
`sample_name`	`String`	-	-
`library_name`	`String`	-	-
`readgroup_name`	`String?`	-	-
`platform_unit`	`String?`	-	-
`run_date`	`String?`	-	-
`platform_name`	`String`	-	-
`sequencing_center`	`String?`	-	-
`additional_picard_options`	`String?`	-	-
4 optional inputs with default values
`cpus`	`Int`	-	2
`mem_gb`	`Int`	-	4
`disk_size`	`Int`	-	750
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"

Outputs

Name	Type	Expression
`unmapped_bam`	`File`	`FastqToUBAM.unmapped_bam`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `FastqToUBAM` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

FastqToUBAM

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flowchart TD
    Start([fastq_to_ubam])
    N1["FastqToUBAM"]
    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_read_utils.wdl" as tasks_read_utils

workflow fastq_to_ubam {
    meta {
        description: "Convert reads from fastq format (single or paired) to unaligned BAM format."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }

    call tasks_read_utils.FastqToUBAM
    output {
        File unmapped_bam = FastqToUBAM.unmapped_bam
    }
}