nextflow-development_skill

Overview

This skill runs nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on local FASTQs or public GEO/SRA datasets to produce gene expression, variant calling, or ATAC-seq peak/coverage results. It guides users through data acquisition, environment validation, test runs, samplesheet creation, pipeline configuration, execution, and output verification. The workflow is designed for bench scientists and researchers without specialist bioinformatics training.

How this skill works

The skill inspects available input (local FASTQ/BAM/CRAM or GSE/GSM/SRR accessions) and helps fetch public data when requested. It runs an environment checker, executes a pipeline test profile, generates or validates a samplesheet, confirms genome and pipeline options, then launches nf-core pipelines via Nextflow with reproducible flags. After completion it verifies key outputs like MultiQC reports, gene count matrices, VCFs, or peak files.

When to use it

• You have local FASTQ files and need standardized analysis (RNA-seq, WGS/WES, ATAC-seq).
• You want to reanalyze a public dataset from GEO/SRA using nf-core pipelines.
• You need automated samplesheet creation and validation for large studies.
• You want a reproducible, pinned-version nf-core run with Docker or Singularity.
• You need stepwise checks and a fail-safe test run before processing full-scale data.

Best practices

• Always run the environment check and resolve any Docker/Nextflow/Java issues before proceeding.
• Run the pipeline test profile and confirm the test completes successfully before using real data.
• Generate and validate the samplesheet; inspect tumor/normal labels for sarek and replicate info for atacseq.
• Confirm and, if necessary, download the correct reference genome before launching a full run.
• Pin pipeline versions with -r and use -resume for safe restarts; limit resources with max_cpus/max_memory when needed.

Example use cases

• Run nf-core/rnaseq on local paired-end FASTQs to produce gene counts and TPMs for differential expression.
• Fetch a GEO study (GSE) by accession, download selected samples, build a samplesheet, and run nf-core/atacseq to call peaks.
• Analyze paired tumor/normal WES samples with nf-core/sarek for somatic variant discovery and produce VCFs.
• Validate environment on a new workstation or HPC using the test profile before processing a cohort.
• Resume a partially completed run after resolving a resource or permission error using Nextflow -resume.