nf-epi2me-labs/wf-transcriptomes

Owned by Roberto Barrero Gumiel
Last updated: Sept 28, 2023
1 min read

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:

Prepare the following ‘launch.pbs’ PBS Pro script:

Submit the script to the cluster:

Monitor the progress of the job: