nextflow
Category: life-sciences · License: Apache-2.0 · Version: 1.2
Tags: Nextflow, nf-core, bioinformatics pipelines, workflow management, genomics
When to use it
Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word “Nextflow”, and for authoring nf-core-compliant pipelines, modules, configs, and linting.Example requests
Ask your agent in plain language, for example:- “how do I resume a nextflow run that crashed halfway?”
- “I’m running nf-core/rnaseq 3.14.0 on our SLURM cluster with Singularity for 24 human paired-end samples. My samplesheet.csv has columns sample,fastq_1,fastq_2,strandedness. The job dies with ‘Process NFCORE_RNASEQ:RNASEQ:STAR_ALIGN terminated with an error exit status (137)’. How do I fix it and keep the finished steps?”
- “I have a pile of tumor/normal exome FASTQs and a reference genome. I want a reproducible, portable analysis setup that can run on my laptop for testing and then scale out to AWS without changing the code, with each tool in its own container. Where do I start?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.