chunk_megablast - WDL Atlas

WORKFLOW chunk_megablast

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

Imports

Namespace	Path
`tools`	`../tasks/tasks_megablast.wdl`

Workflow: chunk_megablast

Chunk megablast function

Author: Broad Viral Genomics

viral-negs@broadinstitute.org

Inputs

Name	Type	Description	Default
`inFasta`	`File`	-	-
`blast_db_tgz`	`File`	-	-
`db_name`	`String`	-	-
`taxidlist`	`File?`	-	-
`log_dir`	`String?`	-	-
9 optional inputs with default values
`tasks`	`String`	-	"megablast"
`chunkSize`	`Int`	-	1000000
`outfmt`	`String`	-	"6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue"
`max_target_seqs`	`Int`	-	1
`output_type`	`String`	-	"full_line"
`machine_mem_gb`	`Int`	-	64
`cpu`	`Int`	-	16
`disk_size_gb`	`Int`	-	300
`docker`	`String`	-	"quay.io/broadinstitute/viral-classify:fn_blast"

Outputs

Name	Type	Expression
`blast_hits`	`File`	`ChunkBlastHits.blast_hits`
`blast_filter_logs`	`File`	`ChunkBlastHits.blast_py_log`
`chunk_blast_runtime`	`File`	`ChunkBlastHits.duration_seconds`
`max_ram_gb`	`Int`	`ChunkBlastHits.max_ram_gb`
`cpu_load`	`String`	`ChunkBlastHits.cpu_load`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `ChunkBlastHits` ↗

Input Mappings (3)

Input	Value
`inFasta`	`inFasta`
`blast_db_tgz`	`blast_db_tgz`
`db_name`	`db_name`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

ChunkBlastHits

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flowchart TD
    Start([chunk_megablast])
    N1["ChunkBlastHits"]
    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_megablast.wdl" as tools

workflow chunk_megablast {
    meta {
        description: "Chunk megablast function"
        author: "Broad Viral Genomics"
        email: "viral-negs@broadinstitute.org"
        allowNestedInputs: true
    }
    input {
        File    inFasta
        File    blast_db_tgz
        String  db_name 
    }
    call tools.ChunkBlastHits {
        input: 
            inFasta = inFasta, 
            blast_db_tgz = blast_db_tgz,
            db_name = db_name
    }
    output {
        File    blast_hits = ChunkBlastHits.blast_hits
        File    blast_filter_logs = ChunkBlastHits.blast_py_log
        File    chunk_blast_runtime = ChunkBlastHits.duration_seconds
        Int     max_ram_gb = ChunkBlastHits.max_ram_gb
        String  cpu_load = ChunkBlastHits.cpu_load
    }
}