genbank_gather
pipes/WDL/workflows/genbank_gather.wdl

WORKFLOW genbank_gather

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

Imports

Namespace Path
ncbi ../tasks/tasks_ncbi.wdl
utils ../tasks/tasks_utils.wdl

Workflow: genbank_gather

Consolidate all genbank submission files for individual genomes into bulk submission packages grouped by submission pathway.

Author: Broad Viral Genomics
viral-ngs@broadinstitute.org

Inputs

Name Type Description Default
genbank_file_manifest Array[String?] - -
genbank_submit_files Array[File?] - -
spuid_base String - -
spuid_namespace String - -
account_name String - -
authors_sbt File - -
3 optional inputs with default values

Outputs

Name Type Expression
ftp_submission_files Array[File] package_genbank_submissions.ftp_submission_files
submit_sqns_clean_zip File? package_genbank_submissions.submit_sqns_clean_zip
submit_sqns_warnings_zip File? package_genbank_submissions.submit_sqns_warnings_zip
num_sqns_clean Int package_genbank_submissions.num_sqns_clean
num_sqns_warnings Int package_genbank_submissions.num_sqns_warnings
submit_fluA_clean_zip File? package_genbank_submissions.submit_fluA_clean_zip
submit_fluA_warnings_zip File? package_genbank_submissions.submit_fluA_warnings_zip
num_fluA_clean Int package_genbank_submissions.num_fluA_clean
num_fluA_warnings Int package_genbank_submissions.num_fluA_warnings
submit_fluB_clean_zip File? package_genbank_submissions.submit_fluB_clean_zip
submit_fluB_warnings_zip File? package_genbank_submissions.submit_fluB_warnings_zip
num_fluB_clean Int package_genbank_submissions.num_fluB_clean
num_fluB_warnings Int package_genbank_submissions.num_fluB_warnings
submit_fluC_clean_zip File? package_genbank_submissions.submit_fluC_clean_zip
submit_fluC_warnings_zip File? package_genbank_submissions.submit_fluC_warnings_zip
num_fluC_clean Int package_genbank_submissions.num_fluC_clean
num_fluC_warnings Int package_genbank_submissions.num_fluC_warnings
submit_sc2_clean_zip File? package_genbank_submissions.submit_sc2_clean_zip
submit_sc2_warnings_zip File? package_genbank_submissions.submit_sc2_warnings_zip
num_sc2_clean Int package_genbank_submissions.num_sc2_clean
num_sc2_warnings Int package_genbank_submissions.num_sc2_warnings
submit_noro_clean_zip File? package_genbank_submissions.submit_noro_clean_zip
submit_noro_warnings_zip File? package_genbank_submissions.submit_noro_warnings_zip
num_noro_clean Int package_genbank_submissions.num_noro_clean
num_noro_warnings Int package_genbank_submissions.num_noro_warnings
submit_dengue_clean_zip File? package_genbank_submissions.submit_dengue_clean_zip
submit_dengue_warnings_zip File? package_genbank_submissions.submit_dengue_warnings_zip
num_dengue_clean Int package_genbank_submissions.num_dengue_clean
num_dengue_warnings Int package_genbank_submissions.num_dengue_warnings

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS package_genbank_submissions ↗

Input Mappings (2)
Input Value
genbank_file_manifest select_all(genbank_file_manifest)
genbank_submit_files select_all(genbank_submit_files)

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • package_genbank_submissions
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genbank_gather - WDL Source Code

version 1.0

import "../tasks/tasks_ncbi.wdl" as ncbi
import "../tasks/tasks_utils.wdl" as utils

workflow genbank_gather {
    meta {
        description: "Consolidate all genbank submission files for individual genomes into bulk submission packages grouped by submission pathway."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }

    input {
        Array[String?]     genbank_file_manifest
        Array[File?]       genbank_submit_files
    }

    call ncbi.package_genbank_submissions {
        input:
            genbank_file_manifest   = select_all(genbank_file_manifest),
            genbank_submit_files    = select_all(genbank_submit_files)
    }

    output {
        Array[File] ftp_submission_files  = package_genbank_submissions.ftp_submission_files
        File? submit_sqns_clean_zip       = package_genbank_submissions.submit_sqns_clean_zip
        File? submit_sqns_warnings_zip    = package_genbank_submissions.submit_sqns_warnings_zip
        Int   num_sqns_clean              = package_genbank_submissions.num_sqns_clean
        Int   num_sqns_warnings           = package_genbank_submissions.num_sqns_warnings
        File? submit_fluA_clean_zip       = package_genbank_submissions.submit_fluA_clean_zip
        File? submit_fluA_warnings_zip    = package_genbank_submissions.submit_fluA_warnings_zip
        Int   num_fluA_clean              = package_genbank_submissions.num_fluA_clean
        Int   num_fluA_warnings           = package_genbank_submissions.num_fluA_warnings
        File? submit_fluB_clean_zip       = package_genbank_submissions.submit_fluB_clean_zip
        File? submit_fluB_warnings_zip    = package_genbank_submissions.submit_fluB_warnings_zip
        Int   num_fluB_clean              = package_genbank_submissions.num_fluB_clean
        Int   num_fluB_warnings           = package_genbank_submissions.num_fluB_warnings
        File? submit_fluC_clean_zip       = package_genbank_submissions.submit_fluC_clean_zip
        File? submit_fluC_warnings_zip    = package_genbank_submissions.submit_fluC_warnings_zip
        Int   num_fluC_clean              = package_genbank_submissions.num_fluC_clean
        Int   num_fluC_warnings           = package_genbank_submissions.num_fluC_warnings
        File? submit_sc2_clean_zip        = package_genbank_submissions.submit_sc2_clean_zip
        File? submit_sc2_warnings_zip     = package_genbank_submissions.submit_sc2_warnings_zip
        Int   num_sc2_clean               = package_genbank_submissions.num_sc2_clean
        Int   num_sc2_warnings            = package_genbank_submissions.num_sc2_warnings
        File? submit_noro_clean_zip       = package_genbank_submissions.submit_noro_clean_zip
        File? submit_noro_warnings_zip    = package_genbank_submissions.submit_noro_warnings_zip
        Int   num_noro_clean              = package_genbank_submissions.num_noro_clean
        Int   num_noro_warnings           = package_genbank_submissions.num_noro_warnings
        File? submit_dengue_clean_zip     = package_genbank_submissions.submit_dengue_clean_zip
        File? submit_dengue_warnings_zip  = package_genbank_submissions.submit_dengue_warnings_zip
        Int   num_dengue_clean            = package_genbank_submissions.num_dengue_clean
        Int   num_dengue_warnings         = package_genbank_submissions.num_dengue_warnings
    }
}