Gene Coverage Per Sample

geneCoveragePerSample · 1 contributor · 2 versions

usage: gene_coverage_per_sample.py [-h] [-l LIST] [-n NAME] [-p PATH] [-b BED]

[-g GENE] [-r REGION] [-f FOLDS] [-d] [-t THREADS]

Gene or region coverage of bam

optional arguments:

-h, --help	show this help message and exit
-l LIST, --list LIST
	List file: A tsv file contains SampleName PathToBedtoolsOutput on each line
-n NAME, --name NAME
	Sample name if list not used
-p PATH, --path PATH
	Path to bedtools output if list not used
-b BED, --bed BED
	(Deprecated option) Bed file
-g GENE, --gene GENE
	Output gene file
-r REGION, --region REGION
	Output region file
-f FOLDS, --folds FOLDS
	Folds, quoted and commna sepparated, default 1,10,20,100
-d, --remove_duplicates
	(Deprecated option) Remove marked duplicates in analysis, default:false
-t THREADS, --threads THREADS
	number of threads, default:32

Quickstart

from janis_bioinformatics.tools.pmac.genecovpersample.versions import GeneCoveragePerSample_0_0_8

wf = WorkflowBuilder("myworkflow")

wf.step(
    "genecoveragepersample_step",
    GeneCoveragePerSample_0_0_8(

    )
)
wf.output("geneFileOut", source=genecoveragepersample_step.geneFileOut)
wf.output("regionFileOut", source=genecoveragepersample_step.regionFileOut)

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.

4. Generate user input files for geneCoveragePerSample:

# user inputs
janis inputs geneCoveragePerSample > inputs.yaml

inputs.yaml

{}

5. Run geneCoveragePerSample with:

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

Information

ID:geneCoveragePerSample URL:https://github.com/PMCC-BioinformaticsCore/scripts/tree/master/performance Versions:0.0.8, 0.0.7 Container:michaelfranklin/pmacutil:0.0.8 Authors:Jiaan Yu Citations:None Created:2020-04-03 00:00:00 Updated:2020-04-03 00:00:00

Outputs

name	type	documentation
geneFileOut	TextFile
regionFileOut	TextFile

Additional configuration (inputs)

name	type	prefix	position	documentation
listFile	Optional<File>	–list		List file: A tsv file contains SampleName PathToBedtoolsOutput on each line
sampleName	Optional<String>	–name		Sample name if list not used
bedtoolsOutputPath	Optional<File>	–path		Path to bedtools output if list not used
outputGeneFile	Optional<Filename>	–gene		Output gene file
outputRegionFile	Optional<Filename>	–region		Output region file
fold	Optional<String>	–fold		Folds, quoted and commna sepparated, default 1,10,20,100
threads	Optional<Integer>	–threads		number of threads, default:32

Workflow Description Language

version development

task geneCoveragePerSample {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File? listFile
    String? sampleName
    File? bedtoolsOutputPath
    String? outputGeneFile
    String? outputRegionFile
    String? fold
    Int? threads
  }
  command <<<
    set -e
    gene_coverage_per_sample.py \
      ~{if defined(listFile) then ("--list '" + listFile + "'") else ""} \
      ~{if defined(sampleName) then ("--name '" + sampleName + "'") else ""} \
      ~{if defined(bedtoolsOutputPath) then ("--path '" + bedtoolsOutputPath + "'") else ""} \
      --gene '~{select_first([outputGeneFile, "generated.gene.txt"])}' \
      --region '~{select_first([outputRegionFile, "generated.region.txt"])}' \
      ~{if defined(fold) then ("--fold '" + fold + "'") else ""} \
      ~{if defined(threads) then ("--threads " + threads) else ''}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "michaelfranklin/pmacutil:0.0.8"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File geneFileOut = select_first([outputGeneFile, "generated.gene.txt"])
    File regionFileOut = select_first([outputRegionFile, "generated.region.txt"])
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Gene Coverage Per Sample
doc: |-
  usage: gene_coverage_per_sample.py [-h] [-l LIST] [-n NAME] [-p PATH] [-b BED]
                                     [-g GENE] [-r REGION] [-f FOLDS] [-d]
                                     [-t THREADS]

  Gene or region coverage of bam

  optional arguments:
    -h, --help            show this help message and exit
    -l LIST, --list LIST  List file: A tsv file contains SampleName
                          PathToBedtoolsOutput on each line
    -n NAME, --name NAME  Sample name if list not used
    -p PATH, --path PATH  Path to bedtools output if list not used
    -b BED, --bed BED     (Deprecated option) Bed file
    -g GENE, --gene GENE  Output gene file
    -r REGION, --region REGION
                          Output region file
    -f FOLDS, --folds FOLDS
                          Folds, quoted and commna sepparated, default
                          1,10,20,100
    -d, --remove_duplicates
                          (Deprecated option) Remove marked duplicates in
                          analysis, default:false
    -t THREADS, --threads THREADS
                          number of threads, default:32


requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: michaelfranklin/pmacutil:0.0.8

inputs:
- id: listFile
  label: listFile
  doc: "List file: A tsv file contains SampleName\tPathToBedtoolsOutput on each line"
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --list
- id: sampleName
  label: sampleName
  doc: Sample name if list not used
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --name
- id: bedtoolsOutputPath
  label: bedtoolsOutputPath
  doc: Path to bedtools output if list not used
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --path
- id: outputGeneFile
  label: outputGeneFile
  doc: Output gene file
  type:
  - string
  - 'null'
  default: generated.gene.txt
  inputBinding:
    prefix: --gene
- id: outputRegionFile
  label: outputRegionFile
  doc: Output region file
  type:
  - string
  - 'null'
  default: generated.region.txt
  inputBinding:
    prefix: --region
- id: fold
  label: fold
  doc: Folds, quoted and commna sepparated, default 1,10,20,100
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --fold
- id: threads
  label: threads
  doc: number of threads, default:32
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --threads

outputs:
- id: geneFileOut
  label: geneFileOut
  type: File
  outputBinding:
    glob: generated.gene.txt
    loadContents: false
- id: regionFileOut
  label: regionFileOut
  type: File
  outputBinding:
    glob: generated.region.txt
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: gene_coverage_per_sample.py
arguments: []

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