A monorepo of Open OnDemand (OOD) apps for running nf-core pipelines on Tufts HPC. It contains:

• dashboard/: a single landing page that lists every installed nf-core pipeline and its versions. It is site-independent and ready to use at any center.
• nf-core--/: Batch Connect launch apps, one per pipeline version. These are Tufts-specific reference apps (see below).

The repository is registered with Appverse as a Monorepo via the root appverse.yml.

> [!IMPORTANT] > Do not copy the nf-core-* apps from this repository to your site. > They were generated for Tufts HPC and contain Tufts-specific paths, modules, partitions, and the tufts nf-core profile. They will not run correctly anywhere else. > > To deploy at your center: > 1. Generate your own apps with nfcore2ood: download the nf-core pipelines you want, then convert them to OOD apps using your site's configuration. > 2. Install the dashboard/ from this repository on top of your generated apps. No changes to the dashboard are needed.

Which parts do I use?

Requirements

• Open OnDemand 3.1 or newer (required by the form behavior that nfcore2ood generates)
• Admin (root/sudo) access to your OOD system apps directory, typically /var/www/ood/apps/sys/
• A site where Nextflow and a container engine (Apptainer/Singularity) are available to compute nodes
• Python 3 on the machine where you run nfcore2ood

Deploying at your center

Step 1: Generate your pipeline apps with nfcore2ood

1. Clone nfcore2ood and create your site configuration:

   git clone https://github.com/TuftsRT/nfcore2ood.git
   cd nfcore2ood
   cp nf2ood.env.example nf2ood.env
   

2. Edit nf2ood.env for your site. The values shipped in the example file are Tufts values. At minimum, set:

   • NF2OOD_PIPELINE_ROOT: where downloaded nf-core pipelines are stored
   • NF2OOD_SINGULARITY_CACHEDIR: your Singularity/Apptainer cache path
   • NF2OOD_PARTITION_YML: a partition snippet matching your scheduler
   • NF2OOD_SLURM_PROFILE: your own institutional profile from nf-core/configs. Do not reuse the Tufts profile.
   • NF2OOD_CLUSTER: your OOD cluster id

   See the nfcore2ood configuration reference for every option.

3. Download the pipelines you want to offer:

   source ./nf2ood.env
   ./download_nfcore_pipeline.sh --name rnaseq --revision 3.26.0
   

4. Generate the OOD apps:

   ./nf2ood --output /path/to/generated-apps
   

   Use --pipeline and --version to regenerate a single app later without rebuilding everything.

Step 2: Install the generated apps

Copy the generated nf-core-- directories into your OOD system apps directory:

sudo cp -r /path/to/generated-apps/nf-core-* /var/www/ood/apps/sys/

Each app should be readable by all users, and its manifest.yml must include a readable name and a subcategory (nfcore2ood writes both).

Step 3: Install the dashboard from this repository

git clone https://github.com/TuftsRT/tufts-ood-nfcore.git

# Install the dashboard app
sudo mkdir -p /var/www/ood/apps/sys/nf-core
sudo cp -r tufts-ood-nfcore/dashboard/. /var/www/ood/apps/sys/nf-core/

# Link its three integration points into the OOD dashboard
sudo ln -s /var/www/ood/apps/sys/nf-core/controllers/nf_pipelines_controller.rb \
  /var/www/ood/apps/sys/dashboard/app/controllers/nf_pipelines_controller.rb

sudo mkdir -p /etc/ood/config/apps/dashboard/views/nf_pipelines
sudo ln -s /var/www/ood/apps/sys/nf-core/views/index.html.erb \
  /etc/ood/config/apps/dashboard/views/nf_pipelines/index.html.erb

sudo mkdir -p /etc/ood/config/apps/dashboard/initializers
sudo ln -s /var/www/ood/apps/sys/nf-core/initializers/nf_core_dashboard_route.rb \
  /etc/ood/config/apps/dashboard/initializers/nf_core_dashboard_route.rb

The symlinks are needed because the dashboard extends the stock OOD dashboard rather than replacing it. See dashboard/README.md for what each file does.

Step 4: Restart the web server and verify

In Open OnDemand, choose Help → Restart Web Server (this restarts your per-user NGINX; restarting Apache alone is not enough). Then open the nf-core dashboard page. Each pipeline you generated should appear, grouped by subcategory, with its versions listed.

How the dashboard finds your apps

The dashboard does not use a hand-maintained catalog. It discovers child apps at runtime, so it expects them to:

• be installed in the OOD system apps directory
• have directory names like nf-core-rnaseq-3-26-0 (nf-core----)
• be Batch Connect apps
• provide name and subcategory in manifest.yml

Apps generated by nfcore2ood follow this convention. Multiple versions of the same pipeline are collapsed into one listing.

Troubleshooting

Reference apps (Tufts deployment)

These apps are what nfcore2ood generates with Tufts configuration. They are provided as examples of the expected output and for Tufts deployment; they are not portable to other sites.

• Ampliseq v2.16.1: amplicon sequencing (16S/ITS) taxonomic profiling
• ChIP-seq v2.1.0: peak-calling and QC
• De Novo Transcript v1.2.1: de novo transcriptome assembly
• Differential Abundance v2.0.0: differential abundance / expression analysis
• FetchNGS v1.12.0: download and prepare public sequencing data (SRA/ENA/GEO)
• Funcscan v3.0.0: functional gene screening (AMR, BGCs)
• MAG v5.4.2: metagenome assembly and binning
• Methylseq v4.1.0: bisulfite sequencing / DNA methylation
• Pathogen Surveillance v1.1.0: pathogen identification, variant calling, surveillance
• Protein Families v2.4.0: protein family generation and annotation
• RNA Fusion v4.1.0: gene fusion detection from RNA-seq
• RNA-seq v3.25.0 and v3.26.0: bulk RNA-seq quantification and QC
• Sarek v3.8.1: germline and somatic variant calling (WGS/WES)
• scRNA-seq v4.1.0: single-cell RNA-seq pre-processing and quantification
• Taxprofiler v2.0.0: taxonomic profiling of metagenomic samples

Repository layout

.
├── appverse.yml                  # Appverse monorepo catalog config
├── dashboard/                    # nf-core landing page (site-independent, use as-is)
└── nf-core--/ # Tufts reference apps (generate your own for other sites)

Related tools

• nfcore2ood: downloads nf-core pipelines and converts them into Open OnDemand apps
• tufts_ood_cache_reset: utility for cache reset

Contributing and support

Questions or problems? Please open an issue. For app-generation problems, include the output of ./nf2ood -V and the relevant part of your nf2ood.env (without sensitive paths).

Maintainer

Tufts Research Technology:

License

MIT. See LICENSE.