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)
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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:
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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. Alternatively, run the following code to copy the sample sheet.csv and launch files:
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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 |
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#!/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 \ --extra_trimgalore_args "--quality 30 --clip_r1 10 --clip_r2 10 --three_prime_clip_r1 1 --three_prime_clip_r2 1 " |
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where:
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Submitting the job
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qsub launch_nf-core_RNAseq_pipeline.pbs |
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