Download Reference microRNA sequences from miRBase
Fetch a copy of microRNA mature sequences:
wget https://www.mirbase.org/download/CURRENT/hairpin.fa gzip -c hairpin.fa > hairpin.fa.gz
Hairpin sequences:
wget https://www.mirbase.org/download/CURRENT/mature.fa gzip -c mature.fa.gz
Run a test
Prior running the pipeline with real data, run the following test:
nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.2.1
To submit the above command to the HPC cluster prepare the following script:
#!/bin/bash -l #PBS -N nfsmrnaseq #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR #load java and set up memory settings to run nextflow module load java NXF_OPTS='-Xms1g -Xmx4g' nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.2.0