Tufts nf-core for Open OnDemand

Open OnDemand apps for running nf-core pipelines on Tufts HPC: a dashboard landing page that groups pipelines by category and collapses versions, plus the individual versioned nf-core-* Batch Connect launch apps.
Repo URL
https://github.com/TuftsRT/tufts-ood-nfcore
Website URL
https://github.com/TuftsRT/tufts-ood-nfcore
Documentation URL
https://nf-co.re
Organization
Tufts University Research Technology
Maintainer name
Tufts Research Technology
Maintainer support URL
https://it.tufts.edu/researchtechnology.tufts.edu
Tags
bioinformatics
Last synced at
Repo README
Tufts nf-core for Open OnDemand

A single repository (monorepo) of Open OnDemand apps for running nf-core pipelines on Tufts HPC. It contains one dashboard landing page plus a set of versioned nf-core-* Batch Connect launch apps, and is registered with Appverse as a Monorepo via the root appverse.yml.

To convert nf-core pipelines into Open OnDemand apps, see our in-house tool nfcore2ood.

The utility for cache reset is available at tufts_ood_cache_reset.

Repository layout

.
├── appverse.yml                  # Appverse monorepo catalog config (lists every app below)
├── dashboard/                    # nf-core landing-page app (app_type: dashboards)
└── nf-core--/ # individual Batch Connect launch apps (app_type: batch-connect-basic)

The dashboard/ app groups pipelines by subcategory, collapses multiple versions of the same pipeline into one listing, and links to each pipeline's launch form. Each nf-core-* directory is a self-contained Batch Connect app (form, submit, and launch templates) that runs one pipeline version.

Apps in this repo

The dashboard plus the following pipeline apps:

  • 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

Deployment

Each nf-core-* app installs and runs as a normal Open OnDemand Batch Connect app. The dashboard/ app is a dashboard integration layer (controller, route initializer, and view) rather than a standalone app — see dashboard/README.md for the symlink-based install steps and runtime assumptions.

Maintainer

Tufts Research Technology — https://it.tufts.edu/researchtechnology.tufts.edu

Apps in this repo