populate_library_and_sample_tables_from_flowcell
pipes/WDL/workflows/populate_library_and_sample_tables_from_flowcell.wdl

WORKFLOW populate_library_and_sample_tables_from_flowcell

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

Imports

Namespace Path
terra ../tasks/tasks_terra.wdl

Workflow: populate_library_and_sample_tables_from_flowcell

Terra only: Populate per-library-lane and per-sample tables from existing demultiplexed flowcell output

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

Inputs

Name Type Description Default
flowcell_run_id String - -
raw_reads_unaligned_bams Array[String] - -
cleaned_reads_unaligned_bams Array[String] - -
meta_by_filename_json File - -
read_counts_raw_json File? - -
read_counts_cleaned_json File? - -
4 optional inputs with default values

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS check_terra_env ↗

No explicit input mappings

CALL TASKS create_or_update_sample_tables ↗

Input Mappings (3)
Input Value
flowcell_run_id flowcell_run_id
workspace_name check_terra_env.workspace_name
workspace_namespace check_terra_env.workspace_namespace

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 2 tasks:
  • check_terra_env
  • create_or_update_sample_tables
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populate_library_and_sample_tables_from_flowcell - Workflow Graph

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populate_library_and_sample_tables_from_flowcell - WDL Source Code

version 1.0

import "../tasks/tasks_terra.wdl" as terra

workflow populate_library_and_sample_tables_from_flowcell {
    meta {
        description: "Terra only: Populate per-library-lane and per-sample tables from existing demultiplexed flowcell output"
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }

    input {
        String flowcell_run_id
    }

    # obtain runtime workspace info necessary to read or change data in
    # Terra tables of the workspace associated with a job
    call terra.check_terra_env

    if(check_terra_env.is_running_on_terra) {
        call terra.create_or_update_sample_tables {
          input:
            flowcell_run_id     = flowcell_run_id,
            workspace_name      = check_terra_env.workspace_name,
            workspace_namespace = check_terra_env.workspace_namespace
        }
    }
}