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taco-simple

This repository implements a read filtering workflow for dahak-taco.

In this documentation we will cover:

  • Download raw sequence data from OSF data store (wget).

  • Assess the quality of the pre-filtered reads (fastqc)

  • Trim and filter the reads based on a quality threshold (trimmomatic)

  • Assess the quality of the post-filtered reads (fastqc)

  • Interleave post-filtered reads (khmer)

We will not cover:

  • How to install taco

  • The basics of taco

For those, see the dahak-taco documentation.

Setting Up Taco

Before you can run any of these workflows, you must first install taco. See dahak-taco documentation for installation instructions.

Once taco is installed, it will be available on the command line. The taco commands covered in this document should be run from the main workflow repository directory.

What's In This Repository

Required directories:

  • rules/ - contains rule and workflow definitions (REQUIRED)

Workflow files:

  • workflow-config/ - contains workflow configuration files
  • workflow-params/ - contains workflow parameter files
  • docker/ - contains custom Docker images for use in taco workflows
  • my-workflow-files/ - directory containing config/param/docker files that should be kept together

Documentation files:

  • docs/ - contains the documentation files (i.e., the document you're reading now)
  • mkdocs.yml - configuration file for mkdocs, the documentation generator used by this repo
  • mkdocs-material-dib/ - git submodule containing mkdocs theme

Optionally, you can also create a directory to contain all of the files for your particular workflow.

Workflows

There's nothing here yet.