alfred
Link to section 'Introduction' of 'alfred' Introduction
Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.
For more information, please check its website: https://biocontainers.pro/tools/alfred and its home page on Github.
Link to section 'Versions' of 'alfred' Versions
- 0.2.5
- 0.2.6
Link to section 'Commands' of 'alfred' Commands
- alfred
Link to section 'Module' of 'alfred' Module
You can load the modules by:
module load biocontainers
module load alfred
Link to section 'Example job' of 'alfred' Example job
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 Alfred on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=alfred
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers alfred
alfred qc -r genome.fasta -o qc.tsv.gz sorted.bam