Oncopipe¶

oncopipe · 11 contributors · 1 version

Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA. The pipeline optionally calls a classifier for B-Cell Acute Lymphocytic Leukaemia (based on AllSorts). As well as variant calling pipeline using Picard,GATK and VEP.

A poster was also presented at ABACBS2018 noting the current status and future plans:

Oncopipe ABACBS 2018

Original code example:

Quickstart¶

from janis_bioinformatics.tools.oshlack.oncopipe.oncopipe import OncopipeWorkflow

wf = WorkflowBuilder("myworkflow")

wf.step(
    "oncopipe_step",
    OncopipeWorkflow(
        name=None,
        reads=None,
        genome_dir=None,
        reference=None,
        gtf=None,
        blacklist=None,
    )
)

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 oncopipe:

# user inputs
janis inputs oncopipe > inputs.yaml

inputs.yaml

blacklist: blacklist
genome_dir: null
gtf: gtf
name: <value>
reads:
- - reads_0.fastq.gz
  - reads_1.fastq.gz
- - reads_0.fastq.gz
  - reads_1.fastq.gz
reference: reference.fasta

Run oncopipe with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`oncopipe`
URL:	No URL to the documentation was provided
Versions:	v0.1.0
Authors:	Rebecca Louise Evans, Breon Schmidt, Andrew Lonsdale, Simon Sadedin, Nadia Davidson, Quarkins, Jovana Maksimovic, Alicia Oshlack, Richard Lupat, Jiaan Yu, Michael Franklin
Citations:
Created:	2020-01-01
Updated:	None

Outputs¶

name	type	documentation

Workflow¶

../../../_images/oncopipe_v0_1_0.dot.png

Embedded Tools¶

Oncopipe: sample preparation OncopipeSamplePreparation/v0.1.0

Additional configuration (inputs)¶

name	type	documentation
name	String	Sample ID
reads	Array<FastqGzPair>
genome_dir	Directory
reference	Fasta
gtf	File
blacklist	File
contigs	Optional<Array<String>>

Workflow Description Language¶

version development

import "tools/OncopipeSamplePreparation_v0_1_0.wdl" as O

workflow oncopipe {
  input {
    String name
    Array[Array[File]] reads
    Directory genome_dir
    File reference
    File gtf
    File blacklist
    Array[String]? contigs
  }
  scatter (r in reads) {
     call O.OncopipeSamplePreparation as process {
      input:
        name=name,
        reads=r,
        genome_dir=genome_dir,
        reference=reference,
        gtf=gtf,
        blacklist=blacklist,
        contigs=contigs
    }
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Oncopipe
doc: |2-

  Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA. The pipeline optionally calls a classifier
  for B-Cell Acute Lymphocytic Leukaemia (based on AllSorts). As well as variant calling pipeline using Picard,GATK and VEP.

  A poster was also presented at ABACBS2018 noting the current status and future plans:

  `Oncopipe ABACBS 2018 <https://atlassian.petermac.org.au/bitbucket/projects/OS/repos/oncopipe/browse/Oncopipe_ABACBS_v6.pdf>`_

  Original code example:

  .. code-block: text

     bpipe run -r        -p name=SAMPLE_ID        -p out=OUTPUT_PATH        -p fastq=FASTQ_GZ_FILES        PATH_TO_THIS_DIR/pipeline/onco.pipe


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

inputs:
- id: name
  doc: Sample ID
  type: string
- id: reads
  type:
    type: array
    items:
      type: array
      items: File
- id: genome_dir
  type: Directory
- id: reference
  type: File
- id: gtf
  type: File
- id: blacklist
  type: File
- id: contigs
  type:
  - type: array
    items: string
  - 'null'

outputs: []

steps:
- id: process
  label: 'Oncopipe: sample preparation'
  in:
  - id: name
    source: name
  - id: reads
    source: reads
  - id: genome_dir
    source: genome_dir
  - id: reference
    source: reference
  - id: gtf
    source: gtf
  - id: blacklist
    source: blacklist
  - id: contigs
    source: contigs
  scatter:
  - reads
  run: tools/OncopipeSamplePreparation_v0_1_0.cwl
  out:
  - id: out_arriba_bam
  - id: out_arriba_fusion
  - id: out_arriba_fusion_discarded
  - id: out_gene_counts
  - id: out_predictions
  - id: out_probabilities
  - id: out_distributions
  - id: out_waterfalls
id: oncopipe