Index Fasta reference¶

IndexFasta · 1 contributor · 1 version

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Quickstart¶

from janis_bioinformatics.tools.common.indexfasta import IndexFasta

wf = WorkflowBuilder("myworkflow")

wf.step(
    "indexfasta_step",
    IndexFasta(
        reference=None,
    )
)
wf.output("out_reference", source=indexfasta_step.out_reference)
wf.output("out_bwa", source=indexfasta_step.out_bwa)
wf.output("out_samtools", source=indexfasta_step.out_samtools)
wf.output("out_dict", source=indexfasta_step.out_dict)

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 IndexFasta:

# user inputs
janis inputs IndexFasta > inputs.yaml

inputs.yaml

reference: reference.fasta

Run IndexFasta with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`IndexFasta`
URL:	No URL to the documentation was provided
Versions:	1.0.0
Authors:	Michael Franklin
Citations:
Created:	2020-02-14
Updated:	2020-11-10

Outputs¶

name	type	documentation
out_reference	FastaWithIndexes
out_bwa	FastaBwa
out_samtools	FastaFai
out_dict	FastDict

Workflow¶

../../../_images/IndexFasta_1_0_0.dot.png

Embedded Tools¶

BWA-Index	`bwaIndex/v0.7.15`
SamTools: faidx	`SamToolsFaidx/1.9.0`
GATK4: CreateSequenceDictionary	`Gatk4CreateSequenceDictionary/4.1.3.0` `join_indexed_fastas/v0.1.0`

Additional configuration (inputs)¶

name	type	documentation
reference	Fasta
bwa_algorithm	Optional<String>
bwa_block_size	Optional<Integer>

Workflow Description Language¶

version development

import "tools/bwaIndex_v0_7_15.wdl" as B
import "tools/SamToolsFaidx_1_9_0.wdl" as S
import "tools/Gatk4CreateSequenceDictionary_4_1_3_0.wdl" as G
import "tools/join_indexed_fastas_v0_1_0.wdl" as J

workflow IndexFasta {
  input {
    File reference
    String? bwa_algorithm = "bwtsw"
    Int? bwa_block_size = 50000000
  }
  call B.bwaIndex as create_bwa {
    input:
      reference=reference,
      blockSize=select_first([bwa_block_size, 50000000]),
      algorithm=select_first([bwa_algorithm, "bwtsw"])
  }
  call S.SamToolsFaidx as create_samtools {
    input:
      reference=reference
  }
  call G.Gatk4CreateSequenceDictionary as create_dict {
    input:
      reference=reference
  }
  call J.join_indexed_fastas as merge {
    input:
      ref_bwa=create_bwa.out,
      ref_bwa_amb=create_bwa.out_amb,
      ref_bwa_ann=create_bwa.out_ann,
      ref_bwa_bwt=create_bwa.out_bwt,
      ref_bwa_pac=create_bwa.out_pac,
      ref_bwa_sa=create_bwa.out_sa,
      ref_samtools=create_samtools.out,
      ref_samtools_fai=create_samtools.out_fai,
      ref_dict=create_dict.out,
      ref_dict_dict=create_dict.out_dict
  }
  output {
    File out_reference = merge.out_reference
    File out_reference_fai = merge.out_reference_fai
    File out_reference_amb = merge.out_reference_amb
    File out_reference_ann = merge.out_reference_ann
    File out_reference_bwt = merge.out_reference_bwt
    File out_reference_pac = merge.out_reference_pac
    File out_reference_sa = merge.out_reference_sa
    File out_reference_dict = merge.out_reference_dict
    File out_bwa = create_bwa.out
    File out_bwa_amb = create_bwa.out_amb
    File out_bwa_ann = create_bwa.out_ann
    File out_bwa_bwt = create_bwa.out_bwt
    File out_bwa_pac = create_bwa.out_pac
    File out_bwa_sa = create_bwa.out_sa
    File out_samtools = create_samtools.out
    File out_samtools_fai = create_samtools.out_fai
    File out_dict = create_dict.out
    File out_dict_dict = create_dict.out_dict
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Index Fasta reference
doc: ''

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement

inputs:
- id: reference
  type: File
- id: bwa_algorithm
  type: string
  default: bwtsw
- id: bwa_block_size
  type: int
  default: 50000000

outputs:
- id: out_reference
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
  outputSource: merge/out_reference
- id: out_bwa
  type: File
  secondaryFiles:
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  outputSource: create_bwa/out
- id: out_samtools
  type: File
  secondaryFiles:
  - pattern: .fai
  outputSource: create_samtools/out
- id: out_dict
  type: File
  secondaryFiles:
  - pattern: ^.dict
  outputSource: create_dict/out

steps:
- id: create_bwa
  label: BWA-Index
  in:
  - id: reference
    source: reference
  - id: blockSize
    source: bwa_block_size
  - id: algorithm
    source: bwa_algorithm
  run: tools/bwaIndex_v0_7_15.cwl
  out:
  - id: out
- id: create_samtools
  label: 'SamTools: faidx'
  in:
  - id: reference
    source: reference
  run: tools/SamToolsFaidx_1_9_0.cwl
  out:
  - id: out
- id: create_dict
  label: 'GATK4: CreateSequenceDictionary'
  in:
  - id: reference
    source: reference
  run: tools/Gatk4CreateSequenceDictionary_4_1_3_0.cwl
  out:
  - id: out
- id: merge
  in:
  - id: ref_bwa
    source: create_bwa/out
  - id: ref_samtools
    source: create_samtools/out
  - id: ref_dict
    source: create_dict/out
  run: tools/join_indexed_fastas_v0_1_0.cwl
  out:
  - id: out_reference
id: IndexFasta