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When the initial trimming is done, verify if any more clipping needs to be done and run the nf-core/rnaseq pipeline that will perform all the steps. For example:
| Code Block |
|---|
#!/bin/bash -l
#PBS -N nfRNAseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=48:00:00
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/rnaseq --input samplesheet.csv \
--outdir results \
-r 3.12.0 \
--genome GRCh38 \
-profile singularity \
--aligner star_salmon \
--extra_trimgalore_args "--clip_r1 10 --clip_r2 10 --three_prime_clip_r1 1 --three_prime_clip_r2 1 " |
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