Usefulaf

Introduction

Usefulaf is an all-in-one Docker/Singularity image for single-cell processing with Alevin-fry(paper). It includes the all tools you need to turn your FASTQ files into a count matrix and then load it into your favorite analysis environment.

For more information, please check:
Docker hub: https://hub.docker.com/r/combinelab/usefulaf
Home page: https://github.com/COMBINE-lab/usefulaf

Versions

  • 0.9.2

Commands

  • simpleaf

  • R

  • Rscript

  • python

  • python3

Module

You can load the modules by:

module load biocontainers
module load usefulaf

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run usefulaf on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=usefulaf
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers usefulaf