Paired-end DNA pipeline

Description

This snakemake pipeline is designed for paired-end NGS DNA

Inputs

• Path of fastqc files
• Name of outout folder
• Reference genome

Outputs

• multiqc_data\ - Dictionary containing the summary results of all the tools, inculde multiqc.html
• logs\ - Directory of log files for each job, check here first if you run into errors
• working\ - Directory containing intermediate files for each job

Workflow

1. **QC--fastqc
2. **Trimming--trim galore
3. **QC--fastqc
4. **Align--bwa
5. **Sort--samtools
6. **Deduplicate--picard
7. **Summary--multiqc

Setup environment

1. Install conda

2. Clone workflow into working directory

   git clone <repo> <dir>
   cd <dir>

3. Create a new enviroment

   conda env create -n <project_name> --file environment.yaml

4. Activate the environment

   conda activate <project_name>

5. Enable the Bioconda channel

   conda config --add channels bioconda
   conda config --add channels conda-forge
   

6. Install snakemake

   conda install snakemake

Run workflow

1. Edit configuration files

   change the path of fastq_dir, output_dir, reference_genome in "config.yaml"

2. Execute the workflow.

• The first time you are executing this snakemake pipeline it should run locally, once the first run is over (you can use --dry), you can switch to running it on the cluster.

  snakemake --configfile "config.yaml" --use-conda  --cores N

3. submit the jobs to SGE cluster to run the pipeline

   download snakemake-executor-plugin-cluster-generic by pip

   pip install snakemake-executor-plugin-cluster-generic

   then

   snakemake --use-conda --jobs {cores}  --executor cluster-generic --cluster-generic-submit-cmd  "qsub -cwd -V -l h_vmem=50G -pe parallel {threads} -o logs/ -e logs/"