SLAW¶

Description¶

SLAW is a scalable, containerized workflow for untargeted LC-MS processing. It was developed by Alexis Delabriere in the Zamboni Lab at ETH Zurich.

Environment Modules¶

Run module spider slaw to find out what environment modules are available for this application.

Environment Variables¶

HPC_SLAW_DIR - installation directory
HPC_SLAW_BIN - executable directory

Additional Usage Information¶

UFRC provides a wrapper script for executing the SLAW workflow inside of its container. As such, you should simply call slaw /path/to/input_dir /path/to/output_dir from within your job script.

For example:

module load slaw/20211217
slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output

This syntax replaces any"docker run ... or singularity run ... commands given in the examples at https://github.com/zamboni-lab/SLAW#quick-start

Job Script Examples¶

#!/bin/bash
#SBATCH --job-name=slaw_test
#SBATCH --mail-type=NONE
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=16gb
#SBATCH --time=01:00:00
#SBATCH --output=slaw_test_%j.log

pwd; hostname; date

module purge
module load slaw

slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output

date

Citation¶

If you publish research that uses SLAW you have to cite it as follows:

Delabriere A, Warmer P, Brennsteiner V and Zamboni N, SLAW: A scalable and self-optimizing processing workflow for untargeted LC-MS, Anal. Chem. 2021 https://doi.org/10.1021/acs.analchem.1c02687

Categories¶

chemistry, spectroscopy