trim_test.pbs

#!/bin/bash
#SBATCH -o splicing.%j.out
#SBATCH -e splicing.%j.err
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=$USER@jax.org
#SBATCH --mem=20000
#SBATCH --cpus-per-task=4
#SBATCH -p compute
#SBATCH -q batch
#SBATCH -t 1-01:00:00


cd $SLURM_SUBMIT_DIR
date;hostname;pwd

module load singularity
curl -fsSL get.nextflow.io | bash

# get the ful length read from config
full_readLen=$(awk '$1=="readlength"{print $3}' NF_splicing_pipeline.config)
echo "read length"
echo ${full_readLen}

# get increment
inc=${increment}
echo "increment"
echo ${inc}

# get new read lengths to test
readLen_1=$(( ${full_readLen} - $(( ${inc} * 1 )) ))
readLen_2=$(( ${full_readLen} - $(( ${inc} * 2 )) ))
readLen_3=$(( ${full_readLen} - $(( ${inc} * 3 )) ))
readLen_4=$(( ${full_readLen} - $(( ${inc} * 4 )) ))

# make list of new read lengths
readlengths="${readLen_1} ${readLen_2} ${readLen_3} ${readLen_4}"
echo "read lengths to test"
echo ${readlengths}

# run testing on all read lengths specified
for readlength in $readlengths; do
   echo $readlength
   ./nextflow run /projects/anczukow-lab/splicing_pipeline/splicing-pipelines-nf/main.nf \
    --readlength $readlength \
    --star_index /projects/anczukow-lab/reference_genomes/human/Gencode/star_overhangs/star_${readlength} \
    --outdir results_${readlength} \
    --test \
    -config NF_splicing_pipeline.config \
    -profile base,sumner \
    --max_memory 200.GB --max_cpus 30 -resume
done