Facets: snp-pileup

FacetsSnpPileup · 2 contributors · 3 versions

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Quickstart

from janis_bioinformatics.tools.facets.snp_pileup.versions import FacetsSnpPileup_0_5_14_1

wf = WorkflowBuilder("myworkflow")

wf.step(
    "facetssnppileup_step",
    FacetsSnpPileup_0_5_14_1(
        vcf_file=None,
        normal=None,
        tumour=None,
    )
)
wf.output("out", source=facetssnppileup_step.out)

OR

  1. Install Janis
  2. Ensure Janis is configured to work with Docker or Singularity.
  3. Ensure all reference files are available:

Note

More information about these inputs are available below.

  1. Generate user input files for FacetsSnpPileup:
# user inputs
janis inputs FacetsSnpPileup > inputs.yaml

inputs.yaml

normal: normal.bam
tumour: tumour.bam
vcf_file: vcf_file.vcf
  1. Run FacetsSnpPileup with:
janis run [...run options] \
    --inputs inputs.yaml \
    FacetsSnpPileup

Information

ID:FacetsSnpPileup
URL:https://github.com/vanallenlab/facets
Versions:0.5.14.1, 0.5.14-2, 0.5.14
Container:vanallenlab/facets:v0.5.14.1
Authors:mumbler, evanwehi
Citations:Ronglai Shen, Venkatraman E. Seshan; FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing, Nucleic Acids Research, Volume 44, Issue 16, 19 September 2016, Pages e131,
DOI:https://doi.org/10.1093/nar/gkw520
Created:2019-12-16
Updated:2019-12-16

Outputs

name type documentation
out File  

Additional configuration (inputs)

name type prefix position documentation
vcf_file VCF   18  
normal IndexedBam   20  
tumour IndexedBam   21  
count_orphans Optional<Boolean> –count-orphans 2 Do not discard anomalous read pairs
ignore_overlaps Optional<Boolean> –ignore-overlaps 4 Disable read-pair overlap detection.
max_depth Optional<Integer> –maxdepth= 6 Sets the maximum depth. Default is 4000.
min_map_quality Optional<Integer> –min-map-quality= 8 Sets the minimum threshold for mapping quality. Default is 0.
min_base_quality Optional<Integer> –min-base-quality= 10 Sets the minimum threshold for base quality. Default is 0.
min_read_counts Optional<String> –min-read-counts= 12 Comma separated list of minimum read counts for a position to be output. Default is 0.
gzip Optional<Boolean> –gzip 14 Compresses the output file with BGZF.
pseudo_snps Optional<String> –pseudo-snps= 16 Every MULTIPLE positions, if there is no SNP,insert a blank record with the total count at theposition.
output_filename Optional<Filename>   19  

Workflow Description Language

version development

task FacetsSnpPileup {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Boolean? count_orphans
    Boolean? ignore_overlaps
    Int? max_depth
    Int? min_map_quality
    Int? min_base_quality
    String? min_read_counts
    Boolean? gzip
    String? pseudo_snps
    File vcf_file
    String? output_filename
    File normal
    File normal_bai
    File tumour
    File tumour_bai
  }
  command <<<
    set -e
    LD_LIBRARY_PATH=/opt/conda/lib /snp-pileup \
      ~{if (defined(count_orphans) && select_first([count_orphans])) then "--count-orphans" else ""} \
      ~{if (defined(ignore_overlaps) && select_first([ignore_overlaps])) then "--ignore-overlaps" else ""} \
      ~{if defined(max_depth) then ("--maxdepth=" + max_depth) else ''} \
      ~{if defined(min_map_quality) then ("--min-map-quality=" + min_map_quality) else ''} \
      ~{if defined(min_base_quality) then ("--min-base-quality=" + min_base_quality) else ''} \
      ~{if defined(min_read_counts) then ("--min-read-counts='" + min_read_counts + "'") else ""} \
      ~{if (defined(gzip) && select_first([gzip])) then "--gzip" else ""} \
      ~{if defined(pseudo_snps) then ("--pseudo-snps='" + pseudo_snps + "'") else ""} \
      '~{vcf_file}' \
      '~{select_first([output_filename, "generated.csv.gz"])}' \
      '~{normal}' \
      '~{tumour}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "vanallenlab/facets:v0.5.14.1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([output_filename, "generated.csv.gz"])
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'Facets: snp-pileup'
doc: ''

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: vanallenlab/facets:v0.5.14.1

inputs:
- id: count_orphans
  label: count_orphans
  doc: Do not discard anomalous read pairs
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --count-orphans
    position: 2
- id: ignore_overlaps
  label: ignore_overlaps
  doc: Disable read-pair overlap detection.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --ignore-overlaps
    position: 4
- id: max_depth
  label: max_depth
  doc: Sets the maximum depth. Default is 4000.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --maxdepth=
    position: 6
    separate: false
- id: min_map_quality
  label: min_map_quality
  doc: Sets the minimum threshold for mapping quality. Default is 0.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --min-map-quality=
    position: 8
    separate: false
- id: min_base_quality
  label: min_base_quality
  doc: Sets the minimum threshold for base quality. Default is 0.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --min-base-quality=
    position: 10
    separate: false
- id: min_read_counts
  label: min_read_counts
  doc: |-
    Comma separated list of minimum read counts for a position to be output. Default is 0.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --min-read-counts=
    position: 12
    separate: false
- id: gzip
  label: gzip
  doc: Compresses the output file with BGZF.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --gzip
    position: 14
- id: pseudo_snps
  label: pseudo_snps
  doc: |-
    Every MULTIPLE positions, if there is no SNP,insert a blank record with the total count at theposition.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --pseudo-snps=
    position: 16
    separate: false
- id: vcf_file
  label: vcf_file
  type: File
  inputBinding:
    position: 18
- id: output_filename
  label: output_filename
  type:
  - string
  - 'null'
  default: generated.csv.gz
  inputBinding:
    position: 19
- id: normal
  label: normal
  type: File
  secondaryFiles:
  - pattern: .bai
  inputBinding:
    position: 20
- id: tumour
  label: tumour
  type: File
  secondaryFiles:
  - pattern: .bai
  inputBinding:
    position: 21

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

baseCommand:
- LD_LIBRARY_PATH=/opt/conda/lib /snp-pileup
arguments: []

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