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Pipelines

Nextflow Tower

This is a guide on how to use Nextflow Tower to monitor nf-core pipeline runs on DanGPU.

All nf-core pipelines have been successfully configured for use on DanGPU.

Getting started

If this is the first time you use Nextflow Tower, sign in and create a personal access token. You need to create a sample sheet before running any nf-core pipeline. Sample sheet format varies according to pipeline and examples can be found in the usage docs:

Running pipelines

Use the helper script nf-core_tower.sh to run DanGPU nf-core configs with Tower.

# Start a new tmux session
tmux new -s session_name

# Export your personal tower access token:
export TOWER_ACCESS_TOKEN=your_access_token

Launch desired nf-core pipeline using helper script. Usage is

nf-core_tower.sh RUNNAME nextflow run <OPTIONS>

As a minimum, the pipeline name, samplesheet location, and genome must be defined, e.g. for rnaseq:

nf-core_tower.sh MYPAPER_2023 nextflow run nf-core/rnaseq -r 3.8.1 --input samplesheet.csv --genome mm10

Tower CLI installation

The tower cli1 is required to be installed only once to connect the DanGPU as a computing resource. Afterward, it's not required any more2.

# Download the latest version of Tower CLI:
wget https://github.com/seqeralabs/tower-cli/releases/download/v0.7.3/tw-0.7.3-linux-x86_64

# Make the file executable and move to directory accessible by $PATH variable:
mkdir ~/.local/bin && mv tw-* tw && chmod +x ~/.local/bin/tw