BWA-Index¶

bwaIndex · 1 contributor · 1 version

bwa - Burrows-Wheeler Alignment Tool Index database sequences in the FASTA format.

Warning: `-a bwtsw’ does not work for short genomes, while `-a is’ and: `-a div’ do not work not for long genomes.

Quickstart¶

from janis_bioinformatics.tools.bwa.index.versions import BwaIndex_0_7_15

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bwaindex_step",
    BwaIndex_0_7_15(
        reference=None,
    )
)
wf.output("out", source=bwaindex_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 bwaIndex:

# user inputs
janis inputs bwaIndex > inputs.yaml

inputs.yaml

reference: reference.fasta

Run bwaIndex with:

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

Information¶

ID:	`bwaIndex`
URL:	http://bio-bwa.sourceforge.net/bwa.shtml#3
Versions:	v0.7.15
Container:	biocontainers/bwa:v0.7.15_cv3
Authors:	Michael Franklin
Citations:	The BWA-MEM algorithm has not been published yet.
Created:	2020-02-14
Updated:	2020-02-14

Outputs¶

name	type	documentation
out	FastaBwa

Additional configuration (inputs)¶

name	type	prefix	position	documentation
reference	Fasta		1
blockSize	Optional<Integer>	-b		block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]
algorithm	Optional<String>	-a		BWT construction algorithm: bwtsw, is or rb2 [auto] is IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. IS is the default algorithm due to its simplicity. The current codes for IS algorithm are reimplemented by Yuta Mori. bwtsw Algorithm implemented in BWT-SW. This method works with the whole human genome.

Workflow Description Language¶

version development

task bwaIndex {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File reference
    Int? blockSize
    String? algorithm
  }
  command <<<
    set -e
    cp -f '~{reference}' '.'
    bwa index \
      ~{if defined(blockSize) then ("-b " + blockSize) else ''} \
      ~{if defined(algorithm) then ("-a '" + algorithm + "'") else ""} \
      '~{basename(reference)}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "biocontainers/bwa:v0.7.15_cv3"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = basename(reference)
    File out_amb = basename(reference) + ".amb"
    File out_ann = basename(reference) + ".ann"
    File out_bwt = basename(reference) + ".bwt"
    File out_pac = basename(reference) + ".pac"
    File out_sa = basename(reference) + ".sa"
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: BWA-Index
doc: |-
  bwa - Burrows-Wheeler Alignment Tool
  Index database sequences in the FASTA format.

  Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
           `-a div' do not work not for long genomes.

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entry: $(inputs.reference)
- class: DockerRequirement
  dockerPull: biocontainers/bwa:v0.7.15_cv3

inputs:
- id: reference
  label: reference
  type: File
  inputBinding:
    position: 1
- id: blockSize
  label: blockSize
  doc: block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -b
- id: algorithm
  label: algorithm
  doc: |
    BWT construction algorithm: bwtsw, is or rb2 [auto]
        - is IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. IS is the default algorithm due to its simplicity. The current codes for IS algorithm are reimplemented by Yuta Mori.
        - bwtsw      Algorithm implemented in BWT-SW. This method works with the whole human genome.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -a

outputs:
- id: out
  label: out
  type: File
  secondaryFiles:
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  outputBinding:
    glob: $(inputs.reference.basename)
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- bwa
- index
arguments: []

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