deplete_only - WDL Atlas

WORKFLOW deplete_only

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

Imports

Namespace	Path
`taxon_filter`	`../tasks/tasks_taxon_filter.wdl`

Workflow: deplete_only

Taxonomic depletion of reads matching unwanted taxa (such as human).

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`raw_reads_unmapped_bam`	`File`	-	-
`bmtaggerDbs`	`Array[File]?`	-	-
`blastDbs`	`Array[File]?`	-	-
`bwaDbs`	`Array[File]?`	-	-
`query_chunk_size`	`Int?`	-	-
5 optional inputs with default values
`clear_tags`	`Boolean`	-	false
`tags_to_clear_space_separated`	`String`	-	"XT X0 X1 XA AM SM BQ CT XN OC OP"
`cpu`	`Int`	-	8
`machine_mem_gb`	`Int`	-	15
`docker`	`String`	-	"quay.io/broadinstitute/viral-classify:2.5.1.0"

Outputs

Name	Type	Expression
`cleaned_bam`	`File`	`deplete_taxa.cleaned_bam`
`cleaned_fastqc`	`File`	`deplete_taxa.cleaned_fastqc`
`cleaned_fastqc_zip`	`File`	`deplete_taxa.cleaned_fastqc_zip`
`depletion_read_count_pre`	`Int`	`deplete_taxa.depletion_read_count_pre`
`depletion_read_count_post`	`Int`	`deplete_taxa.depletion_read_count_post`
`viral_classify_version`	`String`	`deplete_taxa.viralngs_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `deplete_taxa` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

deplete_taxa

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flowchart TD
    Start([deplete_only])
    N1["deplete_taxa"]
    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_taxon_filter.wdl" as taxon_filter

workflow deplete_only {
    meta {
        description: "Taxonomic depletion of reads matching unwanted taxa (such as human)."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call taxon_filter.deplete_taxa

    output {
        File   cleaned_bam               = deplete_taxa.cleaned_bam
        File   cleaned_fastqc            = deplete_taxa.cleaned_fastqc
        File   cleaned_fastqc_zip        = deplete_taxa.cleaned_fastqc_zip
        Int    depletion_read_count_pre  = deplete_taxa.depletion_read_count_pre
        Int    depletion_read_count_post = deplete_taxa.depletion_read_count_post
        String viral_classify_version    = deplete_taxa.viralngs_version
    }
}