BioWDL: QC

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This repository contains a collection of BioWDL workflows which can be used for quality control preprocessing and reporting of sequencing data. The following workflows are available:

• AdapterClipping.wdl: Uses cutadapt to perform adapter clipping.
• QC.wdl: Combines the other workflows in this repository.
• QualityReport.wdl: Uses a number of tools to produce quality reports.

These workflows are part of BioWDL developed by the SASC team.

Usage

QC.wdl can be run using Cromwell:

java -jar cromwell-<version>.jar run -i inputs.json QC.wdl

Input

Inputs are provided through a JSON file. The minimally required inputs are described below, but additional inputs are available. A template containing all possible inputs can be generated using Womtool as described in the WOMtool documentation. See this page for some additional general notes and information about pipeline inputs.

{
  "QC.reads": {
    "R1":"Path to read1",
    "R1_md5": "(Optional) path to read1.md5",
    "R2":"Path to read2",
    "R2_md5": "(Optional) path to read1.md5"
  },
  "QC.outputDir":"Where the results should be output to",
  "QC.alwaysRunAdapterClipping": "Boolean (Optional) Whether adapter clipping should always run. Use this if you want to add custom paramaters for read preprocessing. Defaults to 'false'",
  "QC.sample": "Sample name that will be used in the Seqstat output",
  "QC.library": "Library name that will be used in the Seqstat output",
  "QC.readgroup": "Readgroup that can be used in the Seqstat output"
}

Example

An example of an inputs.json might look like this:

{
  "QC.reads": {
    "R1":"/home/user/samples/sample_1/lib_1/rg_1/R1.fq.gz",
    "R2":"/home/user/samples/sample_1/lib_1/rg_1/R2.fq.gz"
  },
  "QC.outputDir":"/home/user/analysis/QCed_reads/",
  "QC.sample": "sample_1",
  "QC.library": "lib_1",
  "QC.readgroup": "rg_1"
}

Dependency requirements and tool versions

Included in the repository is an environment.yml file. This file includes all the tool version on which the workflow was tested. You can use conda and this file to create an environment with all the correct tools.

Output

A new set of FASTQ files from which detected adapters have been clipped and a set of quality reports.

Contact

For any question related to these workflows, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.