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#!/bin/bash -l
#PBS -N nfrna2
#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'

#run the rnaseq pipeline
#with-dag can output files in .png, .pdf, .svg or .html
nextflow run nf-core/rnaseq -profile conda  --input samplesheet.csv \
        --genome GRCm38 \
        --alignedaligner star_rsemsalmon \
        --min_mapped_reads 5 \
        --clip_r1 10 \
        --clip_r2 10 \
        --three_prime_clip_r1 2 \
        --three_prime_clip_r2 2 \
        --remove_ribo_rna \
        -dump-channels \
        -with-dag flowchart.png