Kallisto-Index¶

kallistoIndex · 1 contributor · 1 version

Builds a kallisto index

Quickstart¶

from janis_bioinformatics.tools.kallisto.index.versions import KallistoIndex_0_46_2

wf = WorkflowBuilder("myworkflow")

wf.step(
    "kallistoindex_step",
    KallistoIndex_0_46_2(
        reference=None,
    )
)
wf.output("out", source=kallistoindex_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 kallistoIndex:

# user inputs
janis inputs kallistoIndex > inputs.yaml

inputs.yaml

reference: reference.fasta

Run kallistoIndex with:

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

Information¶

ID:	`kallistoIndex`
URL:	https://pachterlab.github.io/kallisto/manual.html
Versions:	v0.46.2
Container:	quay.io/biocontainers/kallisto:0.46.2–h4f7b962_1
Authors:	Thomas Conway
Citations:	NL Bray, H Pimentel, P Melsted and L Pachter, Near optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, p 525–527 (2016).
DOI:	https://doi.org/10.1038/nbt.3519
Created:	2020-05-25
Updated:	2020-05-25

Outputs¶

name	type	documentation
out	KallistoIdx

Additional configuration (inputs)¶

name	type	prefix	position	documentation
reference	Fasta		3	Filename for a reference transcriptome
kmer_size	Optional<Integer>	-k	1	k-mer (odd) length (default: 31, max value: 31)
index	Optional<Filename>	-i	2	Filename for the kallisto index to be constructed

Workflow Description Language¶

version development

task kallistoIndex {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Int? kmer_size
    String? index
    File reference
  }
  command <<<
    set -e
    cp -f '~{reference}' '.'
    kallisto index \
      ~{if defined(kmer_size) then ("-k " + kmer_size) else ''} \
      -i '~{select_first([index, "generated.kidx"])}' \
      '~{basename(reference)}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 2, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([index, "generated.kidx"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Kallisto-Index
doc: Builds a kallisto index

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entry: $(inputs.reference)
- class: DockerRequirement
  dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1

inputs:
- id: kmer_size
  label: kmer_size
  doc: 'k-mer (odd) length (default: 31, max value: 31)'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -k
    position: 1
- id: index
  label: index
  doc: Filename for the kallisto index to be constructed
  type:
  - string
  - 'null'
  default: generated.kidx
  inputBinding:
    prefix: -i
    position: 2
- id: reference
  label: reference
  doc: Filename for a reference transcriptome
  type: File
  inputBinding:
    position: 3

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

baseCommand:
- kallisto
- index
arguments: []

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