GATK4: CreateSequenceDictionary

Gatk4CreateSequenceDictionary · 1 contributor · 3 versions

Creates a sequence dictionary for a reference sequence. This tool creates a sequence dictionary file (with “.dict” extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.

The reference sequence can be gzipped (both .fasta and .fasta.gz are supported).

Usage example:

java -jar picard.jar CreateSequenceDictionary

R=reference.fasta O=reference.dict

Quickstart

from janis_bioinformatics.tools.gatk4.createsequencedictionary.versions import Gatk4CreateSequenceDictionary_4_1_4

wf = WorkflowBuilder("myworkflow")

wf.step(
    "gatk4createsequencedictionary_step",
    Gatk4CreateSequenceDictionary_4_1_4(
        reference=None,
    )
)
wf.output("out", source=gatk4createsequencedictionary_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.

4. Generate user input files for Gatk4CreateSequenceDictionary:

# user inputs
janis inputs Gatk4CreateSequenceDictionary > inputs.yaml

inputs.yaml

reference: reference.fasta

5. Run Gatk4CreateSequenceDictionary with:

janis run [...run options] \
    --inputs inputs.yaml \
    Gatk4CreateSequenceDictionary

Information

ID:Gatk4CreateSequenceDictionary URL:https://gatk.broadinstitute.org/hc/en-us/articles/360036509572-CreateSequenceDictionary-Picard- Versions:4.1.4.0, 4.1.3.0, 4.1.2.0 Container:broadinstitute/gatk:4.1.4.0 Authors:Michael Franklin Citations:TBD Created:2020-02-14 Updated:2020-02-14

Outputs

name	type	documentation
out	FastDict	Output reference with ^.dict reference

Additional configuration (inputs)

name	type	prefix	position	documentation
reference	Fasta	–REFERENCE		(-R) Input reference fasta or fasta.gz Required.
javaOptions	Optional<Array<String>>
compression_level	Optional<Integer>			Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.

Workflow Description Language

version development

task Gatk4CreateSequenceDictionary {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[String]? javaOptions
    Int? compression_level
    File reference
  }
  command <<<
    set -e
    cp -f '~{reference}' '.'
    gatk CreateSequenceDictionary \
      --java-options '-Xmx~{((select_first([runtime_memory, 2, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
      --REFERENCE '~{basename(reference)}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 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, 2, 4])}G"
    preemptible: 2
  }
  output {
    File out = basename(reference)
    File out_dict = sub(sub(sub(basename(reference), "\\.fasta$", ".dict"), "\\.fna$", ".dict"), "\\.fa$", ".dict")
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'GATK4: CreateSequenceDictionary'
doc: |-
  Creates a sequence dictionary for a reference sequence.  This tool creates a sequence dictionary file (with ".dict"
  extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools.
  The output file contains a header but no SAMRecords, and the header contains only sequence records.

  The reference sequence can be gzipped (both .fasta and .fasta.gz are supported).

  Usage example:

      java -jar picard.jar CreateSequenceDictionary \
          R=reference.fasta \
          O=reference.dict

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entry: $(inputs.reference)
- 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: reference
  label: reference
  doc: (-R) Input reference fasta or fasta.gz  Required.
  type: File
  inputBinding:
    prefix: --REFERENCE

outputs:
- id: out
  label: out
  doc: Output reference with ^.dict reference
  type: File
  secondaryFiles:
  - pattern: ^.dict
  outputBinding:
    glob: $(inputs.reference.basename)
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- gatk
- CreateSequenceDictionary
arguments:
- prefix: --java-options
  position: -1
  valueFrom: |-
    $("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 2, 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: Gatk4CreateSequenceDictionary