Annotate Bam Stats to Somatic Vcf Workflow¶

AddBamStatsSomatic · 1 contributor · 1 version

No documentation was provided: contribute one

Quickstart¶

from janis_bioinformatics.tools.pmac.addBamStatsSomaticWorkflow import AddBamStatsSomatic_0_1_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "addbamstatssomatic_step",
    AddBamStatsSomatic_0_1_0(
        normal_id=None,
        tumor_id=None,
        normal_bam=None,
        tumor_bam=None,
        reference=None,
        vcf=None,
    )
)
wf.output("out", source=addbamstatssomatic_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 AddBamStatsSomatic:

# user inputs
janis inputs AddBamStatsSomatic > inputs.yaml

inputs.yaml

normal_bam: normal_bam.bam
normal_id: <value>
reference: reference.fasta
tumor_bam: tumor_bam.bam
tumor_id: <value>
vcf: vcf.vcf

Run AddBamStatsSomatic with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`AddBamStatsSomatic`
URL:	No URL to the documentation was provided
Versions:	v0.1.0
Authors:	Jiaan Yu
Citations:
Created:	2020-06-04
Updated:	2020-08-10

Outputs¶

name	type	documentation
out	VCF

Workflow¶

../../../_images/AddBamStatsSomatic_v0_1_0.dot.png

Embedded Tools¶

Add Bam Statistics to Vcf addBamStats/0.0.7

Additional configuration (inputs)¶

name	type	documentation
normal_id	String
tumor_id	String
normal_bam	IndexedBam
tumor_bam	IndexedBam
reference	FastaWithIndexes
vcf	VCF
addbamstats_type	Optional<String>	must be either germline or somatic

Workflow Description Language¶

version development

import "tools/samtools_mpileup_subpipeline.wdl" as S
import "tools/addBamStats_0_0_7.wdl" as A

workflow AddBamStatsSomatic {
  input {
    String normal_id
    String tumor_id
    File normal_bam
    File normal_bam_bai
    File tumor_bam
    File tumor_bam_bai
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
    File vcf
    String? addbamstats_type = "somatic"
  }
  call S.samtools_mpileup_subpipeline as tumor {
    input:
      vcf=vcf,
      bam=tumor_bam,
      bam_bai=tumor_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
  }
  call S.samtools_mpileup_subpipeline as normal {
    input:
      vcf=vcf,
      bam=normal_bam,
      bam_bai=normal_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
  }
  call A.addBamStats as addbamstats {
    input:
      normalMpileup=normal.out,
      tumorMpileup=tumor.out,
      normalID=normal_id,
      tumorID=tumor_id,
      inputVcf=vcf,
      type=select_first([addbamstats_type, "somatic"])
  }
  output {
    File out = addbamstats.out
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Annotate Bam Stats to Somatic Vcf Workflow

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement

inputs:
- id: normal_id
  type: string
- id: tumor_id
  type: string
- id: normal_bam
  type: File
  secondaryFiles:
  - pattern: .bai
- id: tumor_bam
  type: File
  secondaryFiles:
  - pattern: .bai
- id: reference
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
- id: vcf
  type: File
- id: addbamstats_type
  doc: must be either germline or somatic
  type: string
  default: somatic

outputs:
- id: out
  type: File
  outputSource: addbamstats/out

steps:
- id: tumor
  in:
  - id: vcf
    source: vcf
  - id: bam
    source: tumor_bam
  - id: reference
    source: reference
  run: tools/samtools_mpileup_subpipeline.cwl
  out:
  - id: out
- id: normal
  in:
  - id: vcf
    source: vcf
  - id: bam
    source: normal_bam
  - id: reference
    source: reference
  run: tools/samtools_mpileup_subpipeline.cwl
  out:
  - id: out
- id: addbamstats
  label: Add Bam Statistics to Vcf
  in:
  - id: normalMpileup
    source: normal/out
  - id: tumorMpileup
    source: tumor/out
  - id: normalID
    source: normal_id
  - id: tumorID
    source: tumor_id
  - id: inputVcf
    source: vcf
  - id: type
    source: addbamstats_type
  run: tools/addBamStats_0_0_7.cwl
  out:
  - id: out
id: AddBamStatsSomatic