GAMS

Genomic Annotation of Metagenomic Sequences

Introduction

• Pre-process input reads with cutadapt and report with fastqc
• (Optionally) Merge overlapping reads with flash
• Analyse pre-processed reads with centrifuge

Setting up

1. For running the pipeline you first need to have a working conda installation. Most of the calls require the activation of the relevant conda environment, so you will have to create them beforehand. The requirements.yml files can be found in the envs directory.

2. Some biopet tools. Latest versions recommended:

   1. SampleConfig
   2. ExtractAdaptersFastqc

3. Since this is wdl you will also need cromwell for the execution of the (sub)-workflows, which you can find here.

Running the pipeline

Locally:

$ java -jar /path/to/cromwell.<version>.jar run pipeline.wdl -i inputs.json 

On a cluster:

$ java -Dconfig.file=/path/to/cluster.config \
  -jar /path/to/cromwell.<version>.jar \
  run pipeline.wdl -i inputs.json 

For shark users:

$ module load cromwell/31
$ java -Dconfig.file=$CROMWELL_SHARK_CONFIG -jar $CROMWELL_JAR run pipeline.wdl -i INPUTS.json