[RCAC Workshop] Genomics Exchange, Session 4: Running nf-core pipelines on clusters

📅 Date: Tuesday, October 27, 2026
⏰ Time: 11:00 AM – 12:00 PM (EDT)
💻 Location: Online (Microsoft Teams link provided upon registration)
🏫 Instructor: Yucheng Zhang, Tufts University

Please register using the link below to receive email reminders and the Microsoft Teams link; the “I’m interested” button does not provide access.

Who Should Attend

Researchers who want production-quality pipelines for common assays such as RNA-seq and variant calling without writing them from scratch.

What You’ll Learn

Most common bioinformatics analyses have already been built, tested, and peer-reviewed by someone else. nf-core is a community catalog of 150+ production pipelines covering RNA-seq, variant calling, ATAC-seq, single-cell, and metagenomics, all of which run on RCAC clusters with a single command. You don’t write them, and you don’t modify them.

The session covers the following:

• What nf-core is, how to search the catalog, and how to read a pipeline's documentation
• A samplesheet, your parameters, and a profile, the only three things you configure yourself
• Running nf-core/rnaseq end to end, from samplesheet through reference to results
• Reading the MultiQC report and the quality signals worth stopping on
• The best practice for diagnosing a failed run

By the End of the Session, You’ll

• Be able to find and evaluate a pipeline in the nf-core catalog for your own data
• Be able to launch a real pipeline on RCAC clusters
• Be able to write a valid samplesheet, including the absolute-path requirement that trips up most first attempts
• Know which parameters matter, and how to read the MultiQC report before trusting your results
• Know how to diagnose a failed run from the log files, and where to go for help

Level

Intermediate. Session 3 (Nextflow fundamentals) or equivalent experience is recommended.

Register now: Click here to register