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| Code Block |
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#!/bin/bash -l #PBS -N nfrna2 #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/rnaseq -profile conda --input samplesheet.csv --genome GRCm38 --aligned star_rsem --min_mapped_reads 5 |
Additional options:
| Code Block |
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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 \
--aligned star_rsem \
--min_mapped_reads 5 \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 2 \
--three_prime_clip_r2 2 \
-dump-channels \
-with-dag flowchart.png |
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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