The current script executes the mirdeep2 tool by invoking the mirdeep2 singularity container. Because no input options have been given, the only output is the manual of the command miRDeep2.pl
#!/bin/sh -l
#SBATCH --partition=batch
#SBATCH --nodes=1
#SBATCH --job-name="mirdeep2"
#SBATCH --output=my_outp.out
#SBATCH --mail-user=mymail@here.gr
#SBATCH --mail-type=ALL
module purge
module load singularity/3.7.1
singularity exec /mnt/big/containers/singularity/mirdeep.sif miRDeep2.pl -h
# a proper miRDeep2 call would be (please modify properly for sake of your needs):
# singularity exec /mnt/big/containers/singularity/mirdeep.sif miRDeep2.pl reads_collapsed.fa genome.fa \ reads_collapsed_vs_genome.arf miRBase_mmu_v14.fa miRBase_rno_v14.fa precursors_ref_this_species.fa -t Mouse 2>report.log
module unload singularity/3.7.1
