BamSorMaDup¶

bamsormadup · 1 contributor · 1 version

bamsormadup: parallel sorting and duplicate marking

Quickstart¶

from janis_bioinformatics.tools.biobambam.bamsormadup.versions import BamSorMaDup_2_0_87

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bamsormadup_step",
    BamSorMaDup_2_0_87(
        alignedReads=None,
    )
)
wf.output("out", source=bamsormadup_step.out)
wf.output("metrics", source=bamsormadup_step.metrics)

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 bamsormadup:

# user inputs
janis inputs bamsormadup > inputs.yaml

inputs.yaml

alignedReads: alignedReads.bam

Run bamsormadup with:

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

Information¶

ID:	`bamsormadup`
URL:	https://gitlab.com/german.tischler/biobambam2
Versions:	2.0.87
Container:	quay.io/biocontainers/biobambam:2.0.87–1
Authors:	Matthias De Smet (@mattdsm)
Citations:	None
Created:	2020-02-26
Updated:	2020-02-26

Outputs¶

name	type	documentation
out	stdout<BAM>
metrics	File

Additional configuration (inputs)¶

name	type	prefix	position	documentation
alignedReads	BAM		200
outputFilename	Optional<Filename>
level	Optional<Integer>	level=		compression settings for output bam file (-1=zlib default,0=uncompressed,1=fast,9=best)
tempLevel	Optional<Integer>	templevel=		compression settings for temporary bam files (-1=zlib default,0=uncompressed,1=fast,9=best)
threads	Optional<Integer>	threads=		Number of threads. (default = 1)
sortOrder	Optional<String>	SO=		output sort order(coordinate by default)
optMinPixelDif	Optional<Integer>	optminpixeldif=		pixel difference threshold for optical duplicates (patterned flowcell: 12000, unpatterned flowcell: 2500)

Workflow Description Language¶

version development

task bamsormadup {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File alignedReads
    String? outputFilename
    Int? level
    Int? tempLevel
    Int? threads
    String? sortOrder
    Int? optMinPixelDif
  }
  command <<<
    set -e
    bamsormadup \
      ~{if defined(select_first([level, 0])) then ("level=" + select_first([level, 0])) else ''} \
      ~{if defined(select_first([tempLevel, 0])) then ("templevel=" + select_first([tempLevel, 0])) else ''} \
      ~{if defined(select_first([threads, select_first([runtime_cpu, 1])])) then ("threads=" + select_first([threads, select_first([runtime_cpu, 1])])) else ''} \
      ~{if defined(select_first([sortOrder, "coordinate"])) then ("SO='" + select_first([sortOrder, "coordinate"]) + "'") else ""} \
      ~{if defined(select_first([optMinPixelDif, 2500])) then ("optminpixeldif=" + select_first([optMinPixelDif, 2500])) else ''} \
      M= 'metrics.txt' \
      inputformat= 'bam' \
      outputFormat= 'bam' \
      '~{alignedReads}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 4, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "quay.io/biocontainers/biobambam:2.0.87--1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 16, 4])}G"
    preemptible: 2
  }
  output {
    File out = stdout()
    File metrics = glob("metrics.txt")[0]
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: BamSorMaDup
doc: 'bamsormadup: parallel sorting and duplicate marking'

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: quay.io/biocontainers/biobambam:2.0.87--1

inputs:
- id: alignedReads
  label: alignedReads
  type: File
  inputBinding:
    position: 200
- id: outputFilename
  label: outputFilename
  type:
  - string
  - 'null'
  default: generated.bam
- id: level
  label: level
  doc: |-
    compression settings for output bam file (-1=zlib default,0=uncompressed,1=fast,9=best)
  type: int
  default: 0
  inputBinding:
    prefix: level=
    separate: false
- id: tempLevel
  label: tempLevel
  doc: |-
    compression settings for temporary bam files (-1=zlib default,0=uncompressed,1=fast,9=best)
  type: int
  default: 0
  inputBinding:
    prefix: templevel=
    separate: false
- id: threads
  label: threads
  doc: Number of threads. (default = 1)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: threads=
    valueFrom: |-
      $([inputs.runtime_cpu, 4, 1].filter(function (inner) { return inner != null })[0])
    separate: false
- id: sortOrder
  label: sortOrder
  doc: output sort order(coordinate by default)
  type: string
  default: coordinate
  inputBinding:
    prefix: SO=
    separate: false
- id: optMinPixelDif
  label: optMinPixelDif
  doc: |-
    pixel difference threshold for optical duplicates (patterned flowcell: 12000, unpatterned flowcell: 2500)
  type: int
  default: 2500
  inputBinding:
    prefix: optminpixeldif=
    separate: false

outputs:
- id: out
  label: out
  type: stdout
- id: metrics
  label: metrics
  type: File
  outputBinding:
    glob: metrics.txt
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- bamsormadup
arguments:
- prefix: M=
  position: 0
  valueFrom: metrics.txt
  separate: false
- prefix: inputformat=
  position: 0
  valueFrom: bam
  separate: false
- prefix: outputFormat=
  position: 0
  valueFrom: bam
  separate: false

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