Running on DCEG CCAD cluster (SGE)

Prepare the pipeline

• activate the snakemake conda environment created in the installation step

conda activate snakemake

• clone the repository

modify config/samples.txt and config/config.yaml as described in here

• go to workflow directory

cd <cloned repo dir>/workflow

• create a script that looks like this

#!/bin/bash

module load singularity

cd <cloned repo dir>/workflow

snakemake  --profile profiles/ccad --use-singularity --singularity-args "--bind /DCEG" --jobs 100 --latency-wait 300 --rerun-incomplete

submit the script

qsub -q long.q -V -j y -cwd -o ${PWD} <script>

monitor the jobs

The log files are in ```<cloned repo dir>/workflow/logs/```, it is also useful to look at ```<cloned repo dir>/workflow/<script>.o<jobid>``` for snakemake logs

#### Fine tuning the pipeline

- To change the queue a particular rule is being submit to, you can edit the _profiles/ccad/cluster.yaml_ file. For example, adding

HC_call_variants : queue : bigmem.q ```
to the profiles/ccad/cluster.yaml file tells GEMSCAN to submit the HC_call_variants jobs to bigmem.q