GATK4: MergeMutectStats¶

Gatk4MergeMutectStats · 1 contributor · 6 versions

TBD

Quickstart¶

from janis_bioinformatics.tools.gatk4.mergemutectstats.versions import Gatk4MergeMutectStats_4_1_8

wf = WorkflowBuilder("myworkflow")

wf.step(
    "gatk4mergemutectstats_step",
    Gatk4MergeMutectStats_4_1_8(
        statsFiles=None,
    )
)
wf.output("out", source=gatk4mergemutectstats_step.out)

OR

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

Note

More information about these inputs are available below.

Generate user input files for Gatk4MergeMutectStats:

# user inputs
janis inputs Gatk4MergeMutectStats > inputs.yaml

inputs.yaml

statsFiles:
- statsFiles_0.txt
- statsFiles_1.txt

Run Gatk4MergeMutectStats with:

janis run [...run options] \
    --inputs inputs.yaml \
    Gatk4MergeMutectStats

Information¶

ID:	`Gatk4MergeMutectStats`
URL:	TBD
Versions:	4.1.8.1, 4.1.7.0, 4.1.6.0, 4.1.4.0, 4.1.3.0, 4.1.2.0
Container:	broadinstitute/gatk:4.1.8.1
Authors:	Hollizeck Sebastian
Citations:	TBD
Created:	2019-09-09
Updated:	2019-09-09

Outputs¶

name	type	documentation
out	TextFile	Merged callability stats

Additional configuration (inputs)¶

name	type	prefix	position	documentation
statsFiles	Array<TextFile>	–stats	0	Callability stats
javaOptions	Optional<Array<String>>
compression_level	Optional<Integer>			Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
mergedStatsOut	Optional<Filename>	-O	1

Workflow Description Language¶

version development

task Gatk4MergeMutectStats {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[String]? javaOptions
    Int? compression_level
    Array[File] statsFiles
    String? mergedStatsOut
  }
  command <<<
    set -e
    gatk MergeMutectStats \
      --java-options '-Xmx~{((select_first([runtime_memory, 8, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
      ~{if length(statsFiles) > 0 then "--stats '" + sep("' --stats '", statsFiles) + "'" else ""} \
      -O '~{select_first([mergedStatsOut, "generated.txt"])}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "broadinstitute/gatk:4.1.8.1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([mergedStatsOut, "generated.txt"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'GATK4: MergeMutectStats'
doc: TBD

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: broadinstitute/gatk:4.1.8.1

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: statsFiles
  label: statsFiles
  doc: Callability stats
  type:
    type: array
    inputBinding:
      prefix: --stats
    items: File
  inputBinding:
    position: 0
- id: mergedStatsOut
  label: mergedStatsOut
  type:
  - string
  - 'null'
  default: generated.txt
  inputBinding:
    prefix: -O
    position: 1

outputs:
- id: out
  label: out
  doc: Merged callability stats
  type: File
  outputBinding:
    glob: generated.txt
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- gatk
- MergeMutectStats
arguments:
- prefix: --java-options
  position: -1
  valueFrom: |-
    $("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 8, 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: Gatk4MergeMutectStats