orphan:

ParseFastqcAdaptors · 1 contributor · 1 version

Parse overrepresented region and lookup in Cutadapt table

Quickstart

from janis_bioinformatics.tools.pmac.parsefastqc.v0_1_0 import ParseFastqcAdaptors

wf = WorkflowBuilder("myworkflow")

wf.step(
    "parsefastqcadaptors_step",
    ParseFastqcAdaptors(
        fastqc_datafiles=None,
    )
)
wf.output("adaptor_sequences", source=parsefastqcadaptors_step.adaptor_sequences)

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

inputs.yaml

fastqc_datafiles:
- fastqc_datafiles_0
- fastqc_datafiles_1
  1. Run ParseFastqcAdaptors with:
janis run [...run options] \
    --inputs inputs.yaml \
    ParseFastqcAdaptors





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


 :ID: ``ParseFastqcAdaptors``
URL:No URL to the documentation was provided
Versions:v0.1.0
Container:python:3.8.1
Authors:Michael Franklin
Citations:None
Created:2020-01-07 00:00:00
Updated:2020-02-14 00:00:00

name type documentation ================= ============= =============== adaptor_sequences Array<String> ================= ============= ===============

name type documentation ======================== ============== ========================================================================================== fastqc_datafiles Array<File> cutadapt_adaptors_lookup Optional<File> Specifies a file which contains the list of adapter sequences which will

be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored.