Nf-core-mag
nf-core/mag is a bioinformatics best-practice analysis pipeline for assembly, binning and annotation of metagenomes.[1][2]
Using
nf-core/mag uses Nextflow and Singularity. No additional packages need to be installed by the user.
Storage Requirements
nf-core/mag workflows may consume large amounts of disk space, and may exceed the amount in the local disk on all nodes. Use the BeeGFS Scratch File System, instead.
Self-Test
CAUTION nf-core/mag's self-test requires a lot of storage space
(>750 GiB), and may take several hours to complete. Use /scratch
(i.e. BeeGFS); local scratch (i.e. /local/scratch) on all nodes is not
sufficient.
Job script to run a Nextflow local executor within a Slurm job:
#!/bin/bash
#SBATCH --partition=def
#SBATCH --time=48:00:00
#SBATCH --mem=180G
#SBATCH --cpus-per-task=48
module load nextflow
export NXF_SINGULARITY_CACHEDIR=${BEEGFS_TMPDIR}/singularity
mkdir $NXF_SINGULARITY_CACHEDIR
# N.B. $BEEGFS_TMPDIR will be deleted after the job ends
# so, set output directory to somewhere in the group directory structure
cd $BEEGFS_TMPDIR
nextflow run nf-core/mag -profile test_full,singularity --outdir /ifs/groups/somethingGrp/nf-core-mag-test-results