Performance summary workflow (whole genome)

PerformanceSummaryGenome · 1 contributor · 1 version

No documentation was provided: contribute one

Quickstart

from janis_bioinformatics.tools.pmac.performanceSummaryGenomeWorkflow import PerformanceSummaryGenome_0_1_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "performancesummarygenome_step",
    PerformanceSummaryGenome_0_1_0(
        bam=None,
        sample_name=None,
        genome_file=None,
    )
)
wf.output("performanceSummaryOut", source=performancesummarygenome_step.performanceSummaryOut)

OR

1. Install Janis
2. Ensure Janis is configured to work with Docker or Singularity.
3. Ensure all reference files are available:

Note

More information about these inputs are available below.

4. Generate user input files for PerformanceSummaryGenome:

# user inputs
janis inputs PerformanceSummaryGenome > inputs.yaml

inputs.yaml

bam: bam.bam
genome_file: genome_file.txt
sample_name: <value>

5. Run PerformanceSummaryGenome with:

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

Information

URL: No URL to the documentation was provided

ID:PerformanceSummaryGenome URL:No URL to the documentation was provided Versions:v0.1.0 Authors:Jiaan Yu Citations: Created:2020-04-28 Updated:2020-06-12

Outputs

name	type	documentation
performanceSummaryOut	csv

Workflow

Embedded Tools

GATK4: CollectInsertSizeMetrics	Gatk4CollectInsertSizeMetrics/4.1.3.0
SamTools: Flagstat	SamToolsFlagstat/1.9.0
SamTools: View	SamToolsView/1.9.0
BEDTools: genomeCoverageBed	bedtoolsgenomeCoverageBed/v2.29.2
Performance Summary	performanceSummary/0.0.7

Additional configuration (inputs)

name	type	documentation
bam	IndexedBam
sample_name	String
genome_file	TextFile
samtoolsview_doNotOutputAlignmentsWithBitsSet	Optional<String>	Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x’ (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0’ (i.e. /^0[0-7]+/) [0].
performancesummary_genome	Optional<Boolean>	calculate statistics for whole genome data.–target_flagstat must not be speicified

Workflow Description Language

version development

import "tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.wdl" as G
import "tools/SamToolsFlagstat_1_9_0.wdl" as S
import "tools/SamToolsView_1_9_0.wdl" as S2
import "tools/bedtoolsgenomeCoverageBed_v2_29_2.wdl" as B
import "tools/performanceSummary_0_0_7.wdl" as P

workflow PerformanceSummaryGenome {
  input {
    File bam
    File bam_bai
    String sample_name
    File genome_file
    String? samtoolsview_doNotOutputAlignmentsWithBitsSet = "0x400"
    Boolean? performancesummary_genome = true
  }
  call G.Gatk4CollectInsertSizeMetrics as gatk4collectinsertsizemetrics {
    input:
      bam=bam,
      bam_bai=bam_bai
  }
  call S.SamToolsFlagstat as bamflagstat {
    input:
      bam=bam
  }
  call S2.SamToolsView as samtoolsview {
    input:
      doNotOutputAlignmentsWithBitsSet=select_first([samtoolsview_doNotOutputAlignmentsWithBitsSet, "0x400"]),
      sam=bam
  }
  call S.SamToolsFlagstat as rmdupbamflagstat {
    input:
      bam=samtoolsview.out
  }
  call B.bedtoolsgenomeCoverageBed as bedtoolsgenomecoveragebed {
    input:
      inputBam=samtoolsview.out,
      genome=genome_file
  }
  call P.performanceSummary as performancesummary {
    input:
      flagstat=bamflagstat.out,
      collectInsertSizeMetrics=gatk4collectinsertsizemetrics.out,
      coverage=bedtoolsgenomecoveragebed.out,
      outputPrefix=sample_name,
      rmdupFlagstat=rmdupbamflagstat.out,
      genome=select_first([performancesummary_genome, true])
  }
  output {
    File performanceSummaryOut = performancesummary.out
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Performance summary workflow (whole genome)

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement

inputs:
- id: bam
  type: File
  secondaryFiles:
  - pattern: .bai
- id: sample_name
  type: string
- id: genome_file
  type: File
- id: samtoolsview_doNotOutputAlignmentsWithBitsSet
  doc: |-
    Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0].
  type: string
  default: '0x400'
- id: performancesummary_genome
  doc: |-
    calculate statistics for whole genome data.--target_flagstat must not be speicified
  type: boolean
  default: true

outputs:
- id: performanceSummaryOut
  type: File
  outputSource: performancesummary/out

steps:
- id: gatk4collectinsertsizemetrics
  label: 'GATK4: CollectInsertSizeMetrics'
  in:
  - id: bam
    source: bam
  run: tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.cwl
  out:
  - id: out
  - id: outHistogram
- id: bamflagstat
  label: 'SamTools: Flagstat'
  in:
  - id: bam
    source: bam
  run: tools/SamToolsFlagstat_1_9_0.cwl
  out:
  - id: out
- id: samtoolsview
  label: 'SamTools: View'
  in:
  - id: doNotOutputAlignmentsWithBitsSet
    source: samtoolsview_doNotOutputAlignmentsWithBitsSet
  - id: sam
    source: bam
  run: tools/SamToolsView_1_9_0.cwl
  out:
  - id: out
- id: rmdupbamflagstat
  label: 'SamTools: Flagstat'
  in:
  - id: bam
    source: samtoolsview/out
  run: tools/SamToolsFlagstat_1_9_0.cwl
  out:
  - id: out
- id: bedtoolsgenomecoveragebed
  label: 'BEDTools: genomeCoverageBed'
  in:
  - id: inputBam
    source: samtoolsview/out
  - id: genome
    source: genome_file
  run: tools/bedtoolsgenomeCoverageBed_v2_29_2.cwl
  out:
  - id: out
- id: performancesummary
  label: Performance Summary
  in:
  - id: flagstat
    source: bamflagstat/out
  - id: collectInsertSizeMetrics
    source: gatk4collectinsertsizemetrics/out
  - id: coverage
    source: bedtoolsgenomecoveragebed/out
  - id: outputPrefix
    source: sample_name
  - id: rmdupFlagstat
    source: rmdupbamflagstat/out
  - id: genome
    source: performancesummary_genome
  run: tools/performanceSummary_0_0_7.cwl
  out:
  - id: out
id: PerformanceSummaryGenome