nf-core Sarek (v3.8.1)

This directory contains a generated Open OnDemand batch-connect app for running the nf-core pipeline nf-core-sarek version 3.8.1.

Overview

• Pipeline website: https://nf-co.re/sarek
• Pipeline source repository: https://github.com/nf-core/sarek
• App type: Open OnDemand batch connect
• Generated by: nf2ood

This app exposes nf-core pipeline parameters through the Open OnDemand web interface and launches the pipeline with Nextflow on the target HPC system.

Included files

• manifest.yml: Open OnDemand metadata shown in the app catalog
• form.yml.erb: submission form definition built from the pipeline schema
• submit.yml.erb: job submission settings
• template/script.sh.erb: batch job wrapper that runs Nextflow
• template/nf-params.json.erb: rendered Nextflow parameter file

Local review before deployment

This generated app is intended to be a strong starting point, not a drop-in portable package. Review these areas before publishing or deploying it:

1. Confirm the cluster identifier in form.yml.erb matches your Open OnDemand cluster configuration.
2. Confirm the scheduler settings in submit.yml.erb match your site policies.
3. Confirm the runtime assumptions in template/script.sh.erb, especially the Nextflow module name, pipeline root, cache directories, and scheduler profile.
4. Review schema-derived form fields for pipeline-specific wording that may need user-facing cleanup.

Appverse readiness notes

For future Open OnDemand Appverse submission, aim to keep site-specific values isolated to environment variables, documented defaults, or deploy-time config. The generated app already avoids some hardcoded paths, but the scheduler, runtime environment, and pipeline installation layout still need local review.