Annotate Bam Stats to Germline Vcf Workflow¶

AddBamStatsGermline · 1 contributor · 1 version

No documentation was provided: contribute one

Quickstart¶

from janis_bioinformatics.tools.pmac.addBamStatsGermlineWorkflow import AddBamStatsGermline_0_1_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "addbamstatsgermline_step",
    AddBamStatsGermline_0_1_0(
        bam=None,
        vcf=None,
        reference=None,
    )
)
wf.output("out", source=addbamstatsgermline_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 AddBamStatsGermline:

# user inputs
janis inputs AddBamStatsGermline > inputs.yaml

inputs.yaml

bam: bam.bam
reference: reference.fasta
vcf: vcf.vcf

Run AddBamStatsGermline with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`AddBamStatsGermline`
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/AddBamStatsGermline_v0_1_0.dot.png

Embedded Tools¶

SamTools: Mpileup	`SamToolsMpileup/1.9.0`
Add Bam Statistics to Vcf	`addBamStats/0.0.7`

Additional configuration (inputs)¶

name	type	documentation
bam	IndexedBam
vcf	VCF
reference	FastaWithIndexes
samtoolsmpileup_countOrphans	Optional<Boolean>	do not discard anomalous read pairs
samtoolsmpileup_noBAQ	Optional<Boolean>	disable BAQ (per-Base Alignment Quality)
samtoolsmpileup_minBQ	Optional<Integer>	Minimum base quality for a base to be considered [13]
samtoolsmpileup_maxDepth	Optional<Integer>	max per-file depth; avoids excessive memory usage [8000]
addbamstats_type	Optional<String>	must be either germline or somatic

Workflow Description Language¶

version development

import "tools/SamToolsMpileup_1_9_0.wdl" as S
import "tools/addBamStats_0_0_7.wdl" as A

workflow AddBamStatsGermline {
  input {
    File bam
    File bam_bai
    File vcf
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
    Boolean? samtoolsmpileup_countOrphans = true
    Boolean? samtoolsmpileup_noBAQ = true
    Int? samtoolsmpileup_minBQ = 0
    Int? samtoolsmpileup_maxDepth = 10000
    String? addbamstats_type = "germline"
  }
  call S.SamToolsMpileup as samtoolsmpileup {
    input:
      countOrphans=select_first([samtoolsmpileup_countOrphans, true]),
      noBAQ=select_first([samtoolsmpileup_noBAQ, true]),
      maxDepth=select_first([samtoolsmpileup_maxDepth, 10000]),
      positions=vcf,
      minBQ=select_first([samtoolsmpileup_minBQ, 0]),
      reference=reference,
      bam=bam,
      bam_bai=bam_bai
  }
  call A.addBamStats as addbamstats {
    input:
      mpileup=samtoolsmpileup.out,
      inputVcf=vcf,
      type=select_first([addbamstats_type, "germline"])
  }
  output {
    File out = addbamstats.out
  }
}

Common Workflow Language¶

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

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement

inputs:
- id: bam
  type: File
  secondaryFiles:
  - pattern: .bai
- id: vcf
  type: File
- id: reference
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
- id: samtoolsmpileup_countOrphans
  doc: do not discard anomalous read pairs
  type: boolean
  default: true
- id: samtoolsmpileup_noBAQ
  doc: disable BAQ (per-Base Alignment Quality)
  type: boolean
  default: true
- id: samtoolsmpileup_minBQ
  doc: Minimum base quality for a base to be considered [13]
  type: int
  default: 0
- id: samtoolsmpileup_maxDepth
  doc: max per-file depth; avoids excessive memory usage [8000]
  type: int
  default: 10000
- id: addbamstats_type
  doc: must be either germline or somatic
  type: string
  default: germline

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

steps:
- id: samtoolsmpileup
  label: 'SamTools: Mpileup'
  in:
  - id: countOrphans
    source: samtoolsmpileup_countOrphans
  - id: noBAQ
    source: samtoolsmpileup_noBAQ
  - id: maxDepth
    source: samtoolsmpileup_maxDepth
  - id: positions
    source: vcf
  - id: minBQ
    source: samtoolsmpileup_minBQ
  - id: reference
    source: reference
  - id: bam
    source: bam
  run: tools/SamToolsMpileup_1_9_0.cwl
  out:
  - id: out
- id: addbamstats
  label: Add Bam Statistics to Vcf
  in:
  - id: mpileup
    source: samtoolsmpileup/out
  - id: inputVcf
    source: vcf
  - id: type
    source: addbamstats_type
  run: tools/addBamStats_0_0_7.cwl
  out:
  - id: out
id: AddBamStatsGermline