nf-epi2me-labs/wf-transcriptomes

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

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 'outdir' \
        -w 'workspace_dir'

Submit the script to the cluster:

qsub launch.pbs

Monitor the progress of the job:

qjobs

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nf-epi2me-labs/wf-transcriptomes

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