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Overview

• Use modified launch script to run the full pipeline, including trimming parameters based on the QC output.

• Inspect precomputed results

Run full nf-core/rnaseq pipeline

STEP1: copy metadata (sample sheet.csv) into the working folder (run2_RNAseq)

cp $HOME/workshop/2024-2/session4_RNAseq/data/mouse/samplesheet.csv $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq
cd $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq

• Line 1: Copy the samplesheet.csv file to the working directory

• Line 2: move to the working directory

Copy the PBS Pro script to run the nf-core/rnaseq pipeline:

cp $HOME/workshop/2024-2/session4_RNAseq/scripts/launch_nf-core_RNAseq_pipeline.pbs $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq

NOTE: if you had issues with the above lines. You can Alternatively, run the following code to copy the sample sheet.csv and launch script from a shared folder files:

cp /work/training/2024/rnaseq/data/samplesheet.csv $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq
cp /work/training/2024/rnaseq/scripts/launch_nf-core_RNAseq_pipeline.pbs
cd $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq

...

cat launch_nf-core_RNAseq_pipeline.pbs

#!/bin/bash -l

#PBS -N nfRNAseq

#PBS -l select=1:ncpus=2:mem=4gb

#PBS -l walltime=48:00:00

#work on current directory

cd $PBS_O_WORKDIR

#load java and set up memory settings to run nextflow

module load java

export NXF_OPTS='-Xms1g -Xmx4g'

nextflow run nf-core/rnaseq --input samplesheet.csv \

        --outdir results \

        -r 3.14.0 \

        --genome GRCm38-local \

        -profile singularity \

        --aligner star_salmon \

...

Submitting the job

qsub launch_nf-core_RNAseq_pipeline.pbs

...