merge_tar_chunks - WDL Atlas

WORKFLOW merge_tar_chunks

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

Imports

Namespace	Path
`demux`	`../tasks/tasks_demux.wdl`

Workflow: merge_tar_chunks

Combine multiple tar files (possibly compressed by gzip, bz2, lz4, zstd, etc) into a single tar file. Originally meant for combining streaming upload chunks from a sequencing run.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`tar_chunks`	`Array[File]+`	-	-
`out_filename`	`String`	-	-
`machine_mem_gb`	`Int?`	-	-
1 optional input with default value
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"

Outputs

Name	Type	Expression
`combined_tar`	`File`	`merge_tarballs.combined_tar`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `merge_tarballs` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

merge_tarballs

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flowchart TD
    Start([merge_tar_chunks])
    N1["merge_tarballs"]
    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_demux.wdl" as demux

workflow merge_tar_chunks {
    meta {
        description: "Combine multiple tar files (possibly compressed by gzip, bz2, lz4, zstd, etc) into a single tar file. Originally meant for combining streaming upload chunks from a sequencing run."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
    }

    call demux.merge_tarballs
    output {
        File combined_tar = merge_tarballs.combined_tar
    }
}