Whisper-Align¶

whisperAlign · 1 contributor · 1 version

Builds a whisper index

Quickstart¶

from janis_bioinformatics.tools.whisper.align.versions import WhisperAlign_2_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "whisperalign_step",
    WhisperAlign_2_0(
        index=None,
        fastq=None,
    )
)
wf.output("out", source=whisperalign_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 whisperAlign:

# user inputs
janis inputs whisperAlign > inputs.yaml

inputs.yaml

fastq:
- fastq_0.fastq.gz
- fastq_1.fastq.gz
index: index

Run whisperAlign with:

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

Information¶

ID:	`whisperAlign`
URL:	https://github.com/refresh-bio/Whisper
Versions:	v2.0
Container:	drtomc/whisper:2.0
Authors:	Thomas Conway
Citations:	Deorowicz, S., Gudyś, A. (2019) Whisper 2: indel-sensitive short read mapping, biorXiv
DOI:	https://doi.org/10.1101/2019.12.18.881292
Created:	2020-06-16
Updated:	2020-06-16

Outputs¶

name	type	documentation
out	stdout<BAM>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
index	WhisperIdx		2	base name for whisper index
fastq	FastqGzPair		3	Paired end fastq reads

Workflow Description Language¶

version development

task whisperAlign {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File index
    File index_whisper_idxlut_long_dir
    File index_whisper_idxlut_long_rc
    File index_whisper_idxlut_short_dir
    File index_whisper_idxlut_short_rc
    File index_whisper_idxref_seq_desc
    File index_whisper_idxref_seq_dir_pck
    File index_whisper_idxref_seq_rc_pck
    File index_whisper_idxsa_dir
    File index_whisper_idxsa_rc
    Array[File] fastq
  }
  command <<<
    set -e
    whisper -stdout -t 4 -store-BAM \
      '~{index}' \
      ~{if length(fastq) > 0 then "'" + sep("' '", fastq) + "'" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 4, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "drtomc/whisper:2.0"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = stdout()
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Whisper-Align
doc: Builds a whisper index

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: drtomc/whisper:2.0

inputs:
- id: index
  label: index
  doc: base name for whisper index
  type: File
  secondaryFiles:
  - pattern: .whisper_idx.lut_long_dir
  - pattern: .whisper_idx.lut_long_rc
  - pattern: .whisper_idx.lut_short_dir
  - pattern: .whisper_idx.lut_short_rc
  - pattern: .whisper_idx.ref_seq_desc
  - pattern: .whisper_idx.ref_seq_dir_pck
  - pattern: .whisper_idx.ref_seq_rc_pck
  - pattern: .whisper_idx.sa_dir
  - pattern: .whisper_idx.sa_rc
  inputBinding:
    position: 2
- id: fastq
  label: fastq
  doc: Paired end fastq reads
  type:
    type: array
    items: File
  inputBinding:
    position: 3

outputs:
- id: out
  label: out
  type: stdout
stdout: _stdout
stderr: _stderr

baseCommand:
- whisper
- -stdout
- -t
- '4'
- -store-BAM
arguments: []

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