fetch_sra_to_bam
`pipes/WDL/workflows/fetch_sra_to_bam.wdl`

WORKFLOW fetch_sra_to_bam

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

Imports

Namespace	Path
`ncbi_tools`	`../tasks/tasks_ncbi_tools.wdl`
`terra`	`../tasks/tasks_terra.wdl`

Workflow: fetch_sra_to_bam

Retrieve reads from the NCBI Short Read Archive in unaligned BAM format with relevant metadata encoded.

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`email_address`	`String?`	-	-
`SRA_ID`	`String`	-	-
`sample_name`	`String?`	-	-
`ncbi_api_key`	`String?`	-	-
`machine_mem_gb`	`Int?`	-	-
2 optional inputs with default values
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`docker`	`String`	-	"quay.io/broadinstitute/ncbi-tools:2.11.1"

Outputs

Name	Type	Expression
`reads_ubam`	`File`	`Fetch_SRA_to_BAM.reads_ubam`
`sequencing_center`	`String`	`Fetch_SRA_to_BAM.sequencing_center`
`sequencing_platform`	`String`	`Fetch_SRA_to_BAM.sequencing_platform`
`sequencing_platform_model`	`String`	`Fetch_SRA_to_BAM.sequencing_platform_model`
`biosample_accession`	`String`	`Fetch_SRA_to_BAM.biosample_accession`
`library_id`	`String`	`Fetch_SRA_to_BAM.library_id`
`run_date`	`String`	`Fetch_SRA_to_BAM.run_date`
`sample_collection_date`	`String`	`Fetch_SRA_to_BAM.sample_collection_date`
`sample_collected_by`	`String`	`Fetch_SRA_to_BAM.sample_collected_by`
`sample_strain`	`String`	`Fetch_SRA_to_BAM.sample_strain`
`sample_geo_loc`	`String`	`Fetch_SRA_to_BAM.sample_geo_loc`
`sra_metadata`	`File`	`Fetch_SRA_to_BAM.sra_metadata`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `check_terra_env` ↗

No explicit input mappings

CALL TASKS `Fetch_SRA_to_BAM` ↗

Input Mappings (1)

Input	Value
`email_address`	`user_email_address`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

check_terra_env

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

Fetch_SRA_to_BAM

← Back to Index

flowchart TD
    Start([fetch_sra_to_bam])
    N1["check_terra_env"]
    N2["Fetch_SRA_to_BAM"]
    N1 --> N2
    Start --> N1
    N2 --> 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_ncbi_tools.wdl" as ncbi_tools
import "../tasks/tasks_terra.wdl" as terra

workflow fetch_sra_to_bam {
    meta {
        description: "Retrieve reads from the NCBI Short Read Archive in unaligned BAM format with relevant metadata encoded."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }

    input {
        String? email_address
    }

    call terra.check_terra_env

    String? user_email_address = select_first([email_address,check_terra_env.user_email, ""])

    #if(check_terra_env.is_running_on_terra) {
    call ncbi_tools.Fetch_SRA_to_BAM {
        input:
            email_address = user_email_address
    }
    #}
    #if(!check_terra_env.is_running_on_terra) {
    #    call ncbi_tools.Fetch_SRA_to_BAM
    #}

    output {
        File   reads_ubam                = Fetch_SRA_to_BAM.reads_ubam
        String sequencing_center         = Fetch_SRA_to_BAM.sequencing_center
        String sequencing_platform       = Fetch_SRA_to_BAM.sequencing_platform
        String sequencing_platform_model = Fetch_SRA_to_BAM.sequencing_platform_model
        String biosample_accession       = Fetch_SRA_to_BAM.biosample_accession
        String library_id                = Fetch_SRA_to_BAM.library_id
        String run_date                  = Fetch_SRA_to_BAM.run_date
        String sample_collection_date    = Fetch_SRA_to_BAM.sample_collection_date
        String sample_collected_by       = Fetch_SRA_to_BAM.sample_collected_by
        String sample_strain             = Fetch_SRA_to_BAM.sample_strain
        String sample_geo_loc            = Fetch_SRA_to_BAM.sample_geo_loc
        File   sra_metadata              = Fetch_SRA_to_BAM.sra_metadata
    }
}