nextflow_swc_setup.md

Login to Swan

ssh username@swan.unl.edu

Or use Swan OpenOndemand -> Sign in -> "Clusters" tab at top -> Swan Shell Access

Conda environment setup:

cd $WORK
mkdir nf-training 
cd nf-training
cp /work/demo/hccdemo/public/environment.yml .
srun --qos=short --mem=5gb --time=03:00:00 --pty $SHELL
module purge
module load miniforge  nano
mamba env create -n nf-training -f environment.yml

Download Data:

wget --content-disposition https://ndownloader.figshare.com/files/28531743
tar xvf data.tar.gz 
rm data.tar.gz

Scripts:

wget https://github.com//carpentries-incubator/workflows-nextflow/archive/main.zip 

unzip main.zip 'workflows-nextflow-main/episodes/files/scripts*' -d . 

mv workflows-nextflow-main/episodes/files/scripts . 

rm -r workflows-nextflow-main main.zip

Verify everything is setup

pwd

/work/group/username/nf-training

ls

data environment.yml scripts