Source:https://github.com/epi2me-labs/wf-transcriptomes
If necessary update the epi2me-labs/wf-transcriptomes container to the latest version:
module load java nextflow pull epi2me-labs/wf-transcriptomes
Log to the HPC and create a working directory. For example:
$HOME/epi2me-labs/wf-transcriptomes cd $HOME/epi2me-labs/wf-transcriptomes
Download sample data:
wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
Prepare a ‘samplesheet.csv’ file for the above data:
barcode,alias,condition barcode01,sample01,untreated barcode02,sample02,untreated barcode03,sample03,untreated barcode04,sample04,treated barcode05,sample05,treated barcode06,sample06,treated
Prepare the following ‘launch.pbs’ PBS Pro script:
#!/bin/bash -l
#PBS -N wftrasncriptome
#PBS -l select=1:ncpus=4:mem=8gb
#PBS -l walltime=48:00:00
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run epi2me-labs/wf-transcriptomes \
-profile singularity,local \
--fastq 'differential_expression/differential_expression_fastq' \
--transcriptome-source 'precomputed' \
--de_analysis \
--ref_genome 'differential_expression/hg38_chr20.fa' \
--ref_annotation 'differential_expression/gencode.v22.annotation.chr20.gff' \
--direct_rna \
--minimap2_index_opts '-k 15' \
--ref_transcriptome 'differential_expression/ref_transcriptome.fasta' \
--sample_sheet 'samplesheet.csv' \
--out_dir 'outdir2' \
-w 'workspace_dir2'
Submit the script to the cluster:
qsub launch.pbs
Monitor the progress of the job:
qjobs