Examples and Exercises

Lazypipe Usage and Examples

Running Lazypipe on CSC

Lazypipe is available as a preinstalled module on Puhti server at the Finnish Center for Scientific Computing (CSC).

To run main analysis login to CSC Puhti and type:

module load r-env-singularity
module load biokit
module load lazypipe
sbatch-lazypipe -1 mydata/reads_R1.fastq -2 mydata/reads_R2.fastq --hostgen mydata/host_genome.fna.gz --res resdir --sample sampleid --pipe main --anns abv.nt

The script will ask you to type in the accounting project, maximum duration of the job, memory reservation (min 4GB X number_of_cores recommended) and the number of cores reserved. This will create and submit a job scipt to the sbatch job system.


More examples are available at Lazypipe Wiki:

Lazypipe v3:

Lazypipe v2: