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The GAMS (Genomic Annotation of Metagenomic Sequences) pipeline can be used to process metagenomic data. It performs preprocessing and quality control using cutadapt and fastqc, optionally merges overlapping reads using flash and analyses the data using centrifuge.

Usage

In order to run the complete multisample pipeline, you can run pipeline.wdl using Cromwell:

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

The inputs JSON can be generated using WOMtools as described in the WOMtools documentation. Note that not some inputs should not be used! See this page for more information.

The primary inputs are described below, additional inputs (such as precommands and JAR paths) are available. Please use the above mentioned WOMtools command to see all available inputs.

field	type
sampleConfigFiles	Array[File]	The sample configuration file. See more details below.
outputDir	String	The output directory.
sample.centrifugeIndexPrefix	String	Prefix of the Centrifuge index.

All inputs have to be preceded by pipeline.. Type is indicated according to the WDL data types: File should be indicators of file location (a string in JSON). Types ending in ? indicate the input is optional, types ending in + indicate they require at least one element.

Sample configuration

The sample configuration should be a YML file which adheres to the following structure:

samples:
  <sample>:
    libraries:
      <library>:
        readgroups:
          <readgroup>:
              R1: <Path to first-end FastQ file.>
              R1_md5: <MD5 checksum of first-end FastQ file.>
              R2: <Path to second-end FastQ file.>
              R2_md5: <MD5 checksum of second-end FastQ file.>

Replace the text between < > with appropriate values. MD5 values may be omitted and R2 values may be omitted in the case of single-end data. Multiple readgroups can be added per library and multiple libraries may be given per sample.

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

This pipeline will produce a number of directories and files:

• samples: Contains a directory per sample.
  • <sample>: Contains a folder ‘centrifuge’, which contains the centrifuge output. Also contains a directory per library.
    • <library>: Contains a directory per readgroup.
      • <readgroup>: Contains QC metrics and preprocessed FastQ files.

Contact

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