The biomodal pipeline processes FASTQ files generated using the biomodal library preparation kits. The pipeline utilises Nextflow as the orchestration tool.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load biomodal [user@cn3144 ~]$ cd /data/$USER [user@cn3144 user]$ cp -r $BIOMODAL_TEST_DATA . [user@cn3144 user]$ biomodal analyse --work-dir TEST_DATA/nf-work \ --input-path TEST_DATA \ --meta-file TEST_DATA/CEGX_Run_meta.csv \ --output-path TEST_DATA \ --additional-profile deep_seq \ --tag test_demo_data --mode 6bp [user@cn3144 user]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. biomodal.sh). For example:
#!/bin/bash set -e module load biomodal biomodal analyse --work-dir /data/$USER/nf-work \ --input-path /data/$USER/mybiomodaldata \ --meta-file /data/$USER/mybiomodaldata/meta.csv \ --output-path /data/$USER/mybiomodaldata \ --additional-profile deep_seq \ --tag mydata --mode 6bp
Make sure to update the paths according to your data location. Submit this job using the Slurm sbatch command. You do not need to provide large resources to this job since it is the orchestrating job; just provide enough wall time. For example:
sbatch --cpus-per-task=4 --mem=8G --time=2-00:00:00 biomodal.sh