GATK4: GatherBQSRReports

Gatk4GatherBQSRReports · 1 contributor · 4 versions

USAGE: GatherBQSRReports [arguments] Gathers scattered BQSR recalibration reports into a single file Version:4.1.3.0

Quickstart

from janis_bioinformatics.tools.gatk4.gatherbqsrreports.versions import Gatk4GatherBQSRReports_4_1_4

wf = WorkflowBuilder("myworkflow")

wf.step(
    "gatk4gatherbqsrreports_step",
    Gatk4GatherBQSRReports_4_1_4(

    )
)
wf.output("out", source=gatk4gatherbqsrreports_step.out)

OR

  1. Install Janis
  2. Ensure Janis is configured to work with Docker or Singularity.
  3. Ensure all reference files are available:

Note

More information about these inputs are available below.

  1. Generate user input files for Gatk4GatherBQSRReports:
# user inputs
janis inputs Gatk4GatherBQSRReports > inputs.yaml

inputs.yaml

{}
  1. Run Gatk4GatherBQSRReports with:
janis run [...run options] \
    --inputs inputs.yaml \
    Gatk4GatherBQSRReports

Information

ID:Gatk4GatherBQSRReports
URL:No URL to the documentation was provided
Versions:4.1.4.0, 4.1.3.0, 4.1.2.0, 4.0.12.0
Container:broadinstitute/gatk:4.1.4.0
Authors:Michael Franklin
Citations:None
Created:2020-05-18
Updated:2020-05-18

Outputs

name type documentation
out tsv  

Additional configuration (inputs)

name type prefix position documentation
javaOptions Optional<Array<String>>      
compression_level Optional<Integer>     Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
reports Optional<Array<tsv>> –input   (-I) List of scattered BQSR report files This argument must be specified at least once. Required.
outputFilename Optional<Filename> –output   (-O) File to output the gathered file to Required.
arguments_file Optional<File> –arguments_file   read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null.
gatkConfigFile Optional<String> –gatk-config-file   A configuration file to use with the GATK. Default value: null.
gcsMaxRetries Optional<Integer> –gcs-max-retries   (-gcs-retries) If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20.
gcsProjectForRequesterPays Optional<String> –gcs-project-for-requester-pays   Project to bill when accessing ‘requester pays’ buckets. If unset, these buckets cannot be accessed. Default value: .
help Optional<Boolean> –help   (-h) display the help message Default value: false. Possible values: {true, false}
quiet Optional<Boolean> –QUIET   Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false}
tmpDir Optional<Boolean> –tmp-dir   Temp directory to use. Default value: null.
useJdkDeflater Optional<Boolean> –use-jdk-deflater   (-jdk-deflater) Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false}
useJdkInflater Optional<Boolean> –use-jdk-inflater   (-jdk-inflater) Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false}
verbosity Optional<Boolean> –verbosity   (-verbosity) Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG}
version Optional<Boolean> –version   display the version number for this tool Default value: false. Possible values: {true, false}
showhidden Optional<Boolean> –showHidden   (-showHidden) display hidden arguments Default value: false. Possible values: {true, false}

Workflow Description Language

version development

task Gatk4GatherBQSRReports {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[String]? javaOptions
    Int? compression_level
    Array[File]? reports
    String? outputFilename
    File? arguments_file
    String? gatkConfigFile
    Int? gcsMaxRetries
    String? gcsProjectForRequesterPays
    Boolean? help
    Boolean? quiet
    Boolean? tmpDir
    Boolean? useJdkDeflater
    Boolean? useJdkInflater
    Boolean? verbosity
    Boolean? version
    Boolean? showhidden
  }
  command <<<
    set -e
    gatk GatherBQSRReports \
      --java-options '-Xmx~{((select_first([runtime_memory, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
      ~{if (defined(reports) && length(select_first([reports])) > 0) then "--input '" + sep("' --input '", select_first([reports])) + "'" else ""} \
      --output '~{select_first([outputFilename, "generated.recal_data.tsv"])}' \
      ~{if defined(arguments_file) then ("--arguments_file '" + arguments_file + "'") else ""} \
      ~{if defined(gatkConfigFile) then ("--gatk-config-file '" + gatkConfigFile + "'") else ""} \
      ~{if defined(gcsMaxRetries) then ("--gcs-max-retries " + gcsMaxRetries) else ''} \
      ~{if defined(gcsProjectForRequesterPays) then ("--gcs-project-for-requester-pays '" + gcsProjectForRequesterPays + "'") else ""} \
      ~{if (defined(help) && select_first([help])) then "--help" else ""} \
      ~{if (defined(quiet) && select_first([quiet])) then "--QUIET" else ""} \
      ~{if (defined(tmpDir) && select_first([tmpDir])) then "--tmp-dir" else ""} \
      ~{if (defined(useJdkDeflater) && select_first([useJdkDeflater])) then "--use-jdk-deflater" else ""} \
      ~{if (defined(useJdkInflater) && select_first([useJdkInflater])) then "--use-jdk-inflater" else ""} \
      ~{if (defined(verbosity) && select_first([verbosity])) then "--verbosity" else ""} \
      ~{if (defined(version) && select_first([version])) then "--version" else ""} \
      ~{if (defined(showhidden) && select_first([showhidden])) then "--showHidden" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "broadinstitute/gatk:4.1.4.0"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.recal_data.tsv"])
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'GATK4: GatherBQSRReports'
doc: |
  USAGE: GatherBQSRReports [arguments]
  Gathers scattered BQSR recalibration reports into a single file
  Version:4.1.3.0

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: broadinstitute/gatk:4.1.4.0

inputs:
- id: javaOptions
  label: javaOptions
  type:
  - type: array
    items: string
  - 'null'
- id: compression_level
  label: compression_level
  doc: |-
    Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
  type:
  - int
  - 'null'
- id: reports
  label: reports
  doc: |-
    (-I) List of scattered BQSR report files This argument must be specified at least once. Required.
  type:
  - type: array
    inputBinding:
      prefix: --input
      separate: true
    items: File
  - 'null'
  inputBinding: {}
- id: outputFilename
  label: outputFilename
  doc: (-O) File to output the gathered file to Required.
  type:
  - string
  - 'null'
  default: generated.recal_data.tsv
  inputBinding:
    prefix: --output
    separate: true
- id: arguments_file
  label: arguments_file
  doc: |-
    read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null.
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --arguments_file
    separate: true
- id: gatkConfigFile
  label: gatkConfigFile
  doc: 'A configuration file to use with the GATK. Default value: null.'
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --gatk-config-file
    separate: true
- id: gcsMaxRetries
  label: gcsMaxRetries
  doc: |-
    (-gcs-retries)  If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection  Default value: 20.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --gcs-max-retries
    separate: true
- id: gcsProjectForRequesterPays
  label: gcsProjectForRequesterPays
  doc: |2-
     Project to bill when accessing 'requester pays' buckets. If unset, these buckets cannot be accessed.  Default value: .
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --gcs-project-for-requester-pays
    separate: true
- id: help
  label: help
  doc: |-
    (-h) display the help message Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --help
    separate: true
- id: quiet
  label: quiet
  doc: |-
    Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --QUIET
    separate: true
- id: tmpDir
  label: tmpDir
  doc: 'Temp directory to use. Default value: null.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --tmp-dir
    separate: true
- id: useJdkDeflater
  label: useJdkDeflater
  doc: |-
    (-jdk-deflater)  Whether to use the JdkDeflater (as opposed to IntelDeflater)  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --use-jdk-deflater
    separate: true
- id: useJdkInflater
  label: useJdkInflater
  doc: |-
    (-jdk-inflater)  Whether to use the JdkInflater (as opposed to IntelInflater)  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --use-jdk-inflater
    separate: true
- id: verbosity
  label: verbosity
  doc: |-
    (-verbosity)  Control verbosity of logging.  Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --verbosity
    separate: true
- id: version
  label: version
  doc: |-
    display the version number for this tool Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --version
    separate: true
- id: showhidden
  label: showhidden
  doc: |-
    (-showHidden)  display hidden arguments  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --showHidden
    separate: true

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: generated.recal_data.tsv
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- gatk
- GatherBQSRReports
arguments:
- prefix: --java-options
  position: -1
  valueFrom: |-
    $("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 4].filter(function (inner) { return inner != null })[0] * 3) / 4)).replace(/\{compression\}/g, (inputs.compression_level != null) ? ("-Dsamjdk.compress_level=" + inputs.compression_level) : "").replace(/\{otherargs\}/g, [inputs.javaOptions, []].filter(function (inner) { return inner != null })[0].join(" ")))

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: Gatk4GatherBQSRReports