orphan:

GenerateGenomeFileForBedtoolsCoverage · 2 contributors · 1 version

Generate –genome FILE for BedToolsCoverage

Quickstart

from janis_bioinformatics.tools.pmac.generatebedtoolscoveragegenomefile import GenerateGenomeFileForBedtoolsCoverage

wf = WorkflowBuilder("myworkflow")

wf.step(
    "generategenomefileforbedtoolscoverage_step",
    GenerateGenomeFileForBedtoolsCoverage(
        reference=None,
    )
)
wf.output("out", source=generategenomefileforbedtoolscoverage_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 GenerateGenomeFileForBedtoolsCoverage:
# user inputs
janis inputs GenerateGenomeFileForBedtoolsCoverage > inputs.yaml

inputs.yaml

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





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


 :ID: ``GenerateGenomeFileForBedtoolsCoverage``
URL:No URL to the documentation was provided
Versions:v0.1.0
Container:python:3.8.1
Authors:Michael Franklin, Jiaan Yu
Citations:None
Created:2020-07-21 00:00:00
Updated:2020-06-02 00:00:00

name type documentation ====== ======== ================================ out TextFile Genome file for BedToolsCoverage ====== ======== ================================

name type documentation =============== ================ ===================== reference FastDict output_filename Optional<String> Filename to output to =============== ================ =====================