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#!/bin/bash -l
#PBS -N nfrna2
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
RUN_NAME=run1
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/hic -name ${RUN_NAME} -profile singularity -with-dag flowchart.png | tee ${RUN_NAME}.log |
nextflow.config file:
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params {
input = '/work/eresearch_bio/pwg/nextflow/hic/run1-test/data/*_R{1,2}.fastq.gz'
fasta = '/work/eresearch_bio/pwg/nextflow/hic/run1-test/data/W303_SGD_2015_JRIU00000000.fsa'
skip_cool = false
} |
Submitting the job
Once you have created the folder for the run, the input.tsv file, nextflow.config and launch.pbs you are ready to submit.
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