This page provides a basic introduction to Unix commands to HPC users with no previous knowledge.
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Running the nextflow nf-core/rnaseq pipeline
Requirements:
index.csv → a file that provides a list of sample IDs and their associated FASTQ files (read 1 and read 2)
launch.pbs → a script to submit the job to the HPC cluster
Example index.csv file for nf-core/rnaseq version 3.3:
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group,fastq_1,fastq_2,strandedness control_r1,/work/kenna_team/data/raw_data/SRR1039508_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039508_2.fastq.gz,unstranded dex_r1,/work/kenna_team/data/raw_data/SRR1039509_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039509_2.fastq.gz,unstranded control_r2,/work/kenna_team/data/raw_data/SRR1039512_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039512_2.fastq.gz,unstranded dex_r2,/work/kenna_team/data/raw_data/SRR1039513_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039513_2.fastq.gz,unstranded control_r3,/work/kenna_team/data/raw_data/SRR1039516_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039516_2.fastq.gz,unstranded dex_r3,/work/kenna_team/data/raw_data/SRR1039517_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039517_2.fastq.gz,unstranded control_r4,/work/kenna_team/data/raw_data/SRR1039520_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039520_2.fastq.gz,unstranded dex_r4,/work/kenna_team/data/raw_data/SRR1039521_1.fastq.gz,/work/kenna_team/data/raw_data/SRR1039521_2.fastq.gz,unstranded |
Example launch.pbs script:
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#!/bin/bash -l #PBS -N nfrnaseq #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 #Use the current directory to run the workflow cd $PBS_O_WORKDIR module load java NXF_OPTS='-Xms1g -Xmx4g' #run the nextflow RNA-seq pipeline: nextflow run nf-core/rnaseq -profile singularity -r 3.3 --aligner star_salmon --input index.csv --genome GRCh38 -resume |
...
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cp /work/kenna_team/scripts/star_rsem/* . |
Visualizing results
The results generated in the pipeline can be visualized within the ‘results’ folder.
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#go to the results folder - note by default all nextflow pipelines show the key outputs within the'results' folder, while the 'work' folders contains all intermediate files generated during execution.
cd results
#list folders and files
ls |
example output:
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drwxrws--- 2 barrero 4.0K Sep 7 20:05 fastqc/ drwxrws--- 3 barrero 4.0K Sep 7 20:16 trimgalore/ drwxrws--- 3 barrero 23 Sep 9 13:03 multiqc/ drwxrws--- 2 barrero 4.0K Sep 9 13:03 pipeline_info/ drwxrws--- 20 barrero 4.0K Sep 14 23:23 star_rsem/ |
Access the HPC files from your laptop
Mac laptop (note: need to be connected via VPN)
Open the ‘Finder' window
Click on the search file tab and hit “Command + K”
This will open a new window:
type the above to connect to the shared ‘work' space. Then click connect. To access your personal space replace ‘work’ with 'home’.