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GenerateIntervalsByChromosome · 1 contributor · 1 version

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Quickstart

from janis_bioinformatics.tools.pmac.generatintervalsbychromosome.generateintervalsbychromosome import GenerateIntervalsByChromosome

wf = WorkflowBuilder("myworkflow")

wf.step(
    "generateintervalsbychromosome_step",
    GenerateIntervalsByChromosome(
        reference=None,
    )
)
wf.output("out_regions", source=generateintervalsbychromosome_step.out_regions)

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 GenerateIntervalsByChromosome:
# user inputs
janis inputs GenerateIntervalsByChromosome > inputs.yaml

inputs.yaml

reference: reference.fasta
  1. Run GenerateIntervalsByChromosome with:
janis run [...run options] \
    --inputs inputs.yaml \
    GenerateIntervalsByChromosome





 Information
 ------------


 :ID: ``GenerateIntervalsByChromosome``
URL:No URL to the documentation was provided
Versions:v0.1.0
Container:python:3.8.1
Authors:Michael Franklin
Citations:None
Created:2020-10-19 00:00:00
Updated:2020-10-19 00:00:00

name type documentation =========== ========== =============== out_regions Array<bed> =========== ========== ===============

name type documentation =============== ======================= ========================================================================= reference FastDict FASTA reference with ^.dict reference prefix Optional<String> contig prefix, default ‘chr’ allowed_contigs Optional<Array<String>> Limits allowed_contigs to a list, this defaults of Human CHRs, 1-23,X,Y,Z max_size Optional<Integer> Max size of interval, maybe 5000 for VarDict. overlap Optional<Integer> Consider indels spanning regions, so choose single_file Optional<Boolean> Produce a SINGLE .bed file with all the listed regions =============== ======================= =========================================================================