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In the folder you have created for this run create launch.pbs using a text editor (i.e., vim, nano)

Example 1: define input in launch.pbs

#!/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 --input '*_R{1,2}.fastq.gz' -name ${RUN_NAME} -profile singularity -with-dag flowchart.png | tee ${RUN_NAME}.log

Example 2: define input (i.e., FATSQ, genome file) in a separate cextflow.config file

#!/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

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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