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mirdeep2 singularity container

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