demux_only
pipes/WDL/workflows/demux_only.wdl

WORKFLOW demux_only

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

Imports

Namespace Path
tasks_demux ../tasks/tasks_demux.wdl
reports ../tasks/tasks_reports.wdl

Workflow: demux_only

Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory.

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

Inputs

Name Type Description Default
instrument_model_user_specified String? - -
flowcell_tgz File - -
samplesheet File? - -
runinfo File? - -
sequencingCenter String? - -
barcode_columns_to_rev_comp Array[String]? - -
flowcell String? - -
minMismatchDelta Int? - -
maxNoCalls Int? - -
readStructure String? - -
minimumQuality Int? - -
threads Int? - -
runStartDate String? - -
maxRecordsInRam Int? - -
numberOfNegativeControls Int? - -
tileLimit Int? - -
firstTile Int? - -
machine_mem_gb Int? - -
title String? - -
comment String? - -
file_name String? - -
template String? - -
tag String? - -
ignore_analysis_files String? - -
ignore_sample_names String? - -
sample_names File? - -
exclude_modules Array[String]? - -
module_to_use Array[String]? - -
output_data_format String? - -
config File? - -
config_yaml String? - -
25 optional inputs with default values

Outputs

Name Type Expression
raw_reads_unaligned_bams Array[File] illumina_demux.raw_reads_unaligned_bams
demux_metrics File illumina_demux.metrics
demux_commonBarcodes File illumina_demux.commonBarcodes
demux_outlierBarcodes File illumina_demux.outlierBarcodes
multiqc_report_raw File MultiQC.multiqc_report
run_date String illumina_demux.run_info['run_start_date']
run_info Map[String,String] illumina_demux.run_info
run_info_json File illumina_demux.run_info_json
run_id String illumina_demux.run_info['run_id']
run_lane_count String illumina_demux.flowcell_lane_count
instrument_model_inferred String select_first(flatten([[instrument_model_user_specified], [illumina_demux.run_info['sequencer_model']]]))
demux_viral_core_version String illumina_demux.viralngs_version
meta_by_filename Map[String,Map[String,String]] illumina_demux.meta_by_filename
meta_by_sample Map[String,Map[String,String]] illumina_demux.meta_by_sample
meta_by_filename_json File illumina_demux.meta_by_filename_json
meta_by_sample_json File illumina_demux.meta_by_sample_json

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS illumina_demux ↗

No explicit input mappings

CALL TASKS MultiQC ↗

Input Mappings (1)
Input Value
input_files illumina_demux.raw_reads_fastqc_zip

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • illumina_demux
🐳 ~{docker}

~{docker}

Used by 1 task:
  • MultiQC
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demux_only - Workflow Graph

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demux_only - WDL Source Code

version 1.0

import "../tasks/tasks_demux.wdl" as tasks_demux
import "../tasks/tasks_reports.wdl" as reports

workflow demux_only {
    meta {
        description: "Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }

    input {
        String? instrument_model_user_specified
    }

    call tasks_demux.illumina_demux

    call reports.MultiQC {
        input:
            input_files = illumina_demux.raw_reads_fastqc_zip
    }

    output {
        Array[File] raw_reads_unaligned_bams  = illumina_demux.raw_reads_unaligned_bams
        File        demux_metrics             = illumina_demux.metrics
        File        demux_commonBarcodes      = illumina_demux.commonBarcodes
        File        demux_outlierBarcodes     = illumina_demux.outlierBarcodes
        File        multiqc_report_raw        = MultiQC.multiqc_report

        String             run_date           = illumina_demux.run_info['run_start_date']
        Map[String,String] run_info           = illumina_demux.run_info
        File               run_info_json      = illumina_demux.run_info_json
        String             run_id             = illumina_demux.run_info['run_id']
        String             run_lane_count     = illumina_demux.flowcell_lane_count

        String      instrument_model_inferred = select_first(flatten([[instrument_model_user_specified],[illumina_demux.run_info['sequencer_model']]]))
        String      demux_viral_core_version  = illumina_demux.viralngs_version

        Map[String,Map[String,String]] meta_by_filename      = illumina_demux.meta_by_filename
        Map[String,Map[String,String]] meta_by_sample        = illumina_demux.meta_by_sample
        File                           meta_by_filename_json = illumina_demux.meta_by_filename_json
        File                           meta_by_sample_json   = illumina_demux.meta_by_sample_json
    }
}