Merge and Mark Duplicates¶

mergeAndMarkBams · 1 contributor · 3 versions

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Quickstart¶

from janis_bioinformatics.tools.common.mergeandmark.mergeandmark_4_1_3 import MergeAndMarkBams_4_1_3

wf = WorkflowBuilder("myworkflow")

wf.step(
    "mergeandmarkbams_step",
    MergeAndMarkBams_4_1_3(
        bams=None,
    )
)
wf.output("out", source=mergeandmarkbams_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 mergeAndMarkBams:

# user inputs
janis inputs mergeAndMarkBams > inputs.yaml

inputs.yaml

bams:
- bams_0.bam
- bams_1.bam

Run mergeAndMarkBams with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`mergeAndMarkBams`
URL:	No URL to the documentation was provided
Versions:	4.0.12, 4.1.2, 4.1.3
Authors:	Michael Franklin
Citations:
Created:	2019-02-19
Updated:	2020-11-06

Outputs¶

name	type	documentation
out	IndexedBam

Workflow¶

../../../_images/mergeAndMarkBams_4_1_3.dot.png

Embedded Tools¶

GATK4: Merge SAM Files	`Gatk4MergeSamFiles/4.1.3.0`
GATK4: Mark Duplicates	`Gatk4MarkDuplicates/4.1.3.0`

Additional configuration (inputs)¶

name	type	documentation
bams	Array<IndexedBam>
createIndex	Optional<Boolean>
maxRecordsInRam	Optional<Integer>
sampleName	Optional<String>
mergeSamFiles_useThreading	Optional<Boolean>	Option to create a background thread to encode, compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases runtime by ~20% when writing out a compressed BAM file.
mergeSamFiles_validationStringency	Optional<String>	Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.The –VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values: [STRICT, LENIENT, SILENT]

Workflow Description Language¶

version development

import "tools/Gatk4MergeSamFiles_4_1_3_0.wdl" as G
import "tools/Gatk4MarkDuplicates_4_1_3_0.wdl" as G2

workflow mergeAndMarkBams {
  input {
    Array[File] bams
    Array[File] bams_bai
    Boolean? createIndex = true
    Int? maxRecordsInRam = 5000000
    String? sampleName
    Boolean? mergeSamFiles_useThreading = true
    String? mergeSamFiles_validationStringency = "SILENT"
  }
  call G.Gatk4MergeSamFiles as mergeSamFiles {
    input:
      bams=bams,
      bams_bai=bams_bai,
      sampleName=sampleName,
      useThreading=select_first([mergeSamFiles_useThreading, true]),
      createIndex=select_first([createIndex, true]),
      maxRecordsInRam=select_first([maxRecordsInRam, 5000000]),
      validationStringency=select_first([mergeSamFiles_validationStringency, "SILENT"])
  }
  call G2.Gatk4MarkDuplicates as markDuplicates {
    input:
      bam=[mergeSamFiles.out],
      outputPrefix=sampleName,
      createIndex=select_first([createIndex, true]),
      maxRecordsInRam=select_first([maxRecordsInRam, 5000000])
  }
  output {
    File out = markDuplicates.out
    File out_bai = markDuplicates.out_bai
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Merge and Mark Duplicates
doc: ''

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement

inputs:
- id: bams
  type:
    type: array
    items: File
  secondaryFiles:
  - pattern: .bai
- id: createIndex
  type: boolean
  default: true
- id: maxRecordsInRam
  type: int
  default: 5000000
- id: sampleName
  type:
  - string
  - 'null'
- id: mergeSamFiles_useThreading
  doc: |-
    Option to create a background thread to encode, compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases runtime by ~20% when writing out a compressed BAM file.
  type: boolean
  default: true
- id: mergeSamFiles_validationStringency
  doc: |-
    Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values: [STRICT, LENIENT, SILENT]
  type: string
  default: SILENT

outputs:
- id: out
  type: File
  secondaryFiles:
  - pattern: .bai
  outputSource: markDuplicates/out

steps:
- id: mergeSamFiles
  label: 'GATK4: Merge SAM Files'
  in:
  - id: bams
    source: bams
  - id: sampleName
    source: sampleName
  - id: useThreading
    source: mergeSamFiles_useThreading
  - id: createIndex
    source: createIndex
  - id: maxRecordsInRam
    source: maxRecordsInRam
  - id: validationStringency
    source: mergeSamFiles_validationStringency
  run: tools/Gatk4MergeSamFiles_4_1_3_0.cwl
  out:
  - id: out
- id: markDuplicates
  label: 'GATK4: Mark Duplicates'
  in:
  - id: bam
    source:
    - mergeSamFiles/out
    linkMerge: merge_nested
  - id: outputPrefix
    source: sampleName
  - id: createIndex
    source: createIndex
  - id: maxRecordsInRam
    source: maxRecordsInRam
  run: tools/Gatk4MarkDuplicates_4_1_3_0.cwl
  out:
  - id: out
  - id: metrics
id: mergeAndMarkBams