Sequenza: bam2seqz¶

SeqzBam2Seqz · 2 contributors · 2 versions

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Quickstart¶

from janis_bioinformatics.tools.sequenza.bam2seqz.versions import SequenzaBam2Seqz_3_0_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "seqzbam2seqz_step",
    SequenzaBam2Seqz_3_0_0(
        normal=None,
        tumour=None,
        wiggle_file=None,
        fasta_reference=None,
    )
)
wf.output("out", source=seqzbam2seqz_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 SeqzBam2Seqz:

# user inputs
janis inputs SeqzBam2Seqz > inputs.yaml

inputs.yaml

fasta_reference: fasta_reference.fasta
normal: normal.bam
tumour: tumour.bam
wiggle_file: wiggle_file

Run SeqzBam2Seqz with:

janis run [...run options] \
    --inputs inputs.yaml \
    SeqzBam2Seqz

Information¶

ID:	`SeqzBam2Seqz`
URL:	http://www.cbs.dtu.dk/biotools/sequenza/
Versions:	3.0.0, 2.2.0.9000
Container:	sequenza/sequenza:3.0.0
Authors:	mumbler, evanwehi
Citations:	None
Created:	2019-12-10
Updated:	2019-12-10

Outputs¶

name	type	documentation
out	File

Additional configuration (inputs)¶

name	type	prefix	position	documentation
normal	IndexedBam	–normal	2	Name of the BAM/pileup file from the reference/normal sample
tumour	IndexedBam	–tumor	4	Name of the BAM/pileup file from the reference/normal sample
wiggle_file	File	-gc	6	The GC-content wiggle file
fasta_reference	FastaFai	–fasta	8	The reference FASTA file used to generate the intermediate pileup. Required when input are BAM
output_filename	Optional<Filename>	–output	10	Name of the output file. To use gzip compression name the file ending in .gz. Default STDOUT.

Workflow Description Language¶

version development

task SeqzBam2Seqz {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File normal
    File normal_bai
    File tumour
    File tumour_bai
    File wiggle_file
    File fasta_reference
    File fasta_reference_fai
    String? output_filename
  }
  command <<<
    set -e
    sequenza-utils bam2seqz \
      --normal '~{normal}' \
      --tumor '~{tumour}' \
      -gc '~{wiggle_file}' \
      --fasta '~{fasta_reference}' \
      --output '~{select_first([output_filename, "generated.gz"])}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "sequenza/sequenza:3.0.0"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([output_filename, "generated.gz"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'Sequenza: bam2seqz'
doc: ''

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: sequenza/sequenza:3.0.0

inputs:
- id: normal
  label: normal
  doc: Name of the BAM/pileup file from the reference/normal sample
  type: File
  secondaryFiles:
  - pattern: .bai
  inputBinding:
    prefix: --normal
    position: 2
- id: tumour
  label: tumour
  doc: Name of the BAM/pileup file from the reference/normal sample
  type: File
  secondaryFiles:
  - pattern: .bai
  inputBinding:
    prefix: --tumor
    position: 4
- id: wiggle_file
  label: wiggle_file
  doc: The GC-content wiggle file
  type: File
  inputBinding:
    prefix: -gc
    position: 6
- id: fasta_reference
  label: fasta_reference
  doc: |-
    The reference FASTA file used to generate the intermediate pileup. Required when input are BAM
  type: File
  secondaryFiles:
  - pattern: .fai
  inputBinding:
    prefix: --fasta
    position: 8
- id: output_filename
  label: output_filename
  doc: |-
    Name of the output file. To use gzip compression name the file ending in .gz. Default STDOUT.
  type:
  - string
  - 'null'
  default: generated.gz
  inputBinding:
    prefix: --output
    position: 10

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

baseCommand:
- sequenza-utils
- bam2seqz
arguments: []

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: SeqzBam2Seqz