SamTools: Index¶

SamToolsIndex · 1 contributor · 2 versions

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Quickstart¶

from janis_bioinformatics.tools.samtools.index.versions import SamToolsIndex_1_9

wf = WorkflowBuilder("myworkflow")

wf.step(
    "samtoolsindex_step",
    SamToolsIndex_1_9(
        bam=None,
    )
)
wf.output("out", source=samtoolsindex_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 SamToolsIndex:

# user inputs
janis inputs SamToolsIndex > inputs.yaml

inputs.yaml

bam: null

Run SamToolsIndex with:

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

Information¶

ID:	`SamToolsIndex`
URL:	http://www.htslib.org/doc/samtools.html#COMMANDS_AND_OPTIONS
Versions:	1.9.0, 1.7.0
Container:	quay.io/biocontainers/samtools:1.9–h8571acd_11
Authors:	Michael Franklin
Citations:	None
Created:	2019-12-17
Updated:	2019-12-17

Outputs¶

name	type	documentation
out	IndexedBam

Additional configuration (inputs)¶

name	type	prefix	position	documentation
bam	Union<BAM, SAM, CRAM>		10
threads	Optional<Integer>	-@	10

Workflow Description Language¶

version development

task SamToolsIndex {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File bam
    Int? threads
  }
  command <<<
    set -e
    samtools index \
      '-b' \
      ~{basename(bam)} \
      ~{if defined(select_first([threads, select_first([runtime_cpu, 1])])) then ("-@ " + select_first([threads, select_first([runtime_cpu, 1])])) else ''}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "quay.io/biocontainers/samtools:1.9--h8571acd_11"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = basename(bam)
    File out_bai = basename(bam) + ".bai"
  }
}

Common Workflow Language¶

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

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11

inputs:
- id: bam
  label: bam
  type: File
  inputBinding:
    position: 10
- id: threads
  label: threads
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -@
    position: 10
    valueFrom: $([inputs.runtime_cpu, 1].filter(function (inner) { return inner !=
      null })[0])

outputs:
- id: out
  label: out
  type: File
  secondaryFiles:
  - pattern: .bai
  outputBinding:
    glob: $(inputs.bam)
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- samtools
- index
arguments:
- position: 4
  valueFrom: -b

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