Usage

When starting a new Lazypipe project, you must initialize the project directory by issuing the command init_lazypipe_project from within the new project directory. This will set up the project directory properly to point its resource folders to the application installation directory. This command is only necessary once when you initially create the project directory, but it will not cause any harm if you run it multiple times.

An example (assumes the new Lazypipe project is in a folder called /blue/mygroup/share/test_project/ and that the .fastq and host genomes are already in there):

$ cd /blue/mygroup/share/test_project/

$ module load lazypipe/1.2

$ init_lazypipe_project

$ pipeline.pl \
    -1 /blue/mygroup/share/test_project/data/M15/M15_R1.fastq \
    --hostgen /blue/mygroup/share/test_project/genomes_host/GCA_900108605.1_NNQGG.v01_genomic.fna.gz \
    --res /blue/mygroup/share/test_project/results \
    --label M15 \
    --numth $SLURM_CPUS_PER_TASK \
    --inlen 300 \
    --pipe 1:7,11:13