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#!/bin/bash -l #PBS -N nfsmrnaseq #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 cd $PBS_O_WORKDIR module load java NXF_OPTS='-Xms1g -Xmx4g' nextflow run nf-core/smrnaseq -r 2.1.0 \ -profile singularity \ --outdir outdir \ --input samplesheet.csv \ --genome GRCh38 \ --three_prime_adapter 'AACTGTAGGCACCATCAAT'\ --fastp_min_length 18 \ --fastp_max_length 30 \ --hairpin /work/trtp/data/mirbase/hairpin.fa \ --mature /work/trtp/data/mirbase/mature.fa |
Submit the job to the HPC cluster:
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qsub launch_phase3.pbs |
monitor Monitor the progress on the HPC:
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qjobs |
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