Annotate GATK3 DepthOfCoverage Workflow¶

AnnotateDepthOfCoverage · 1 contributor · 1 version

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Quickstart¶

from janis_bioinformatics.tools.pmac.annotateDepthOfCoverageWorkflow import AnnotateDepthOfCoverage_0_1_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "annotatedepthofcoverage_step",
    AnnotateDepthOfCoverage_0_1_0(
        bam=None,
        bed=None,
        reference=None,
        sample_name=None,
    )
)
wf.output("out", source=annotatedepthofcoverage_step.out)
wf.output("out_sample_summary", source=annotatedepthofcoverage_step.out_sample_summary)

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 AnnotateDepthOfCoverage:

# user inputs
janis inputs AnnotateDepthOfCoverage > inputs.yaml

inputs.yaml

bam: bam.bam
bed: bed.bed
reference: reference.fasta
sample_name: <value>

Run AnnotateDepthOfCoverage with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`AnnotateDepthOfCoverage`
URL:	No URL to the documentation was provided
Versions:	v0.1.0
Authors:	Jiaan Yu
Citations:
Created:	2020-04-28
Updated:	2020-10-07

Outputs¶

name	type	documentation
out	TextFile
out_sample_summary	TextFile

Workflow¶

../../../_images/AnnotateDepthOfCoverage_v0_1_0.dot.png

Embedded Tools¶

GATK3 DepthOfCoverage: Determine coverage at different levels of partitioning and aggregation.	`Gatk3DepthOfCoverage/3.8-1`
Add Sym to DepthOfCoverage	`addSymToDepthOfCoverage/0.0.7`

Additional configuration (inputs)¶

name	type	documentation
bam	IndexedBam
bed	bed
reference	FastaWithIndexes
sample_name	String
gatk3depthofcoverage_countType	Optional<String>	overlapping reads from the same fragment be handled? (COUNT_READS\|COUNT_FRAGMENTS\|COUNT_FRAGMENTS_REQUIRE_SAME_BASE)
gatk3depthofcoverage_summaryCoverageThreshold	Optional<Array<Integer>>	Coverage threshold (in percent) for summarizing statistics

Workflow Description Language¶

version development

import "tools/Gatk3DepthOfCoverage_3_8_1.wdl" as G
import "tools/addSymToDepthOfCoverage_0_0_7.wdl" as A

workflow AnnotateDepthOfCoverage {
  input {
    File bam
    File bam_bai
    File bed
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
    String sample_name
    String? gatk3depthofcoverage_countType = "COUNT_FRAGMENTS_REQUIRE_SAME_BASE"
    Array[Int]? gatk3depthofcoverage_summaryCoverageThreshold = [1, 50, 100, 300, 500]
  }
  call G.Gatk3DepthOfCoverage as gatk3depthofcoverage {
    input:
      bam=bam,
      bam_bai=bam_bai,
      reference=reference,
      reference_fai=reference_fai,
      reference_amb=reference_amb,
      reference_ann=reference_ann,
      reference_bwt=reference_bwt,
      reference_pac=reference_pac,
      reference_sa=reference_sa,
      reference_dict=reference_dict,
      outputPrefix=sample_name,
      intervals=bed,
      countType=select_first([gatk3depthofcoverage_countType, "COUNT_FRAGMENTS_REQUIRE_SAME_BASE"]),
      summaryCoverageThreshold=select_first([gatk3depthofcoverage_summaryCoverageThreshold, [1, 50, 100, 300, 500]])
  }
  call A.addSymToDepthOfCoverage as addsymtodepthofcoverage {
    input:
      inputFile=gatk3depthofcoverage.sampleIntervalSummary,
      outputFilename=sample_name,
      bed=bed
  }
  output {
    File out = addsymtodepthofcoverage.out
    File out_sample_summary = gatk3depthofcoverage.sampleSummary
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Annotate GATK3 DepthOfCoverage Workflow

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement

inputs:
- id: bam
  type: File
  secondaryFiles:
  - pattern: .bai
- id: bed
  type: File
- id: reference
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
- id: sample_name
  type: string
- id: gatk3depthofcoverage_countType
  doc: |-
    overlapping reads from the same  fragment be handled? (COUNT_READS|COUNT_FRAGMENTS|COUNT_FRAGMENTS_REQUIRE_SAME_BASE)
  type: string
  default: COUNT_FRAGMENTS_REQUIRE_SAME_BASE
- id: gatk3depthofcoverage_summaryCoverageThreshold
  doc: Coverage threshold (in percent) for summarizing statistics
  type:
    type: array
    items: int
  default:
  - 1
  - 50
  - 100
  - 300
  - 500

outputs:
- id: out
  type: File
  outputSource: addsymtodepthofcoverage/out
- id: out_sample_summary
  type: File
  outputSource: gatk3depthofcoverage/sampleSummary

steps:
- id: gatk3depthofcoverage
  label: |-
    GATK3 DepthOfCoverage: Determine coverage at different levels of partitioning and aggregation.
  in:
  - id: bam
    source: bam
  - id: reference
    source: reference
  - id: outputPrefix
    source: sample_name
  - id: intervals
    source: bed
  - id: countType
    source: gatk3depthofcoverage_countType
  - id: summaryCoverageThreshold
    source: gatk3depthofcoverage_summaryCoverageThreshold
  run: tools/Gatk3DepthOfCoverage_3_8_1.cwl
  out:
  - id: sample
  - id: sampleCumulativeCoverageCounts
  - id: sampleCumulativeCoverageProportions
  - id: sampleIntervalStatistics
  - id: sampleIntervalSummary
  - id: sampleStatistics
  - id: sampleSummary
- id: addsymtodepthofcoverage
  label: Add Sym to DepthOfCoverage
  in:
  - id: inputFile
    source: gatk3depthofcoverage/sampleIntervalSummary
  - id: outputFilename
    source: sample_name
  - id: bed
    source: bed
  run: tools/addSymToDepthOfCoverage_0_0_7.cwl
  out:
  - id: out
id: AnnotateDepthOfCoverage