Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO r

nf core Pipeline Deployment Run nf core bioinformatics pipelines on local or public sequencing data. Target users: Bench scientists and researchers without specialized bioinformatics training who need to run large scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis. Workflow Checklist Step 0: Acquire Data (GEO/SRA Only) Skip this step if user has local FASTQ files. For public datasets, fetch from GEO/SRA first. See [references/geo sra acquisition.md](references/geo sra acquisition.md) for the full workflow. Quick start: DECISION POINT: After fetching study info, confirm with user: Which sample subset to download (if multiple data types) Suggested genome and pipeline Then continue to Step 1. Step 1: Environment Check Run first. Pipeline will fail without passing environment. All critical checks must pass. If any fail, provide fix instructions: Docker issues Problem Fix Not installed Install from https://docs.docker.com/get docker/ Permission denied sudo usermod aG docker $USER then re login Daemon not running sudo systemctl start docker Nextflow issues Problem Fix Not installed curl s https://get.nextflow.io \ bash && mv nextflow ~/bin/ Version < 23.04 nextflow self update Java issues Problem Fix Not installed / < 11 sudo apt install openjdk 11 jdk Do not proceed until all checks pass. For HPC/Singularity, see [references/troubleshooting.md](references/troubleshooting.md). Step 2: Select Pipeline DECISION POINT: Confirm with user before proceeding. Data Type Pipeline Version Goal RNA seq rnaseq 3.22.2 Gene expression WGS/WES sarek 3.7.1 Variant calling ATAC seq atacseq 2.1.2 Chromatin accessibility Auto detect from data: For pipeline specific details: [references/pipelines/rnaseq.md](references/pipelines/rnaseq.md) [references/pipelines/sarek.md](references/pipelines/sarek.md) [references/pipelines/atacseq.md](references/pipelines/atacseq.md) Step 3: Run Test Profile Validates environment with small data. MUST pass before real data. Pipeline Command rnaseq nextflow run nf core/rnaseq r 3.22.2 profile test,docker outdir test rnaseq sarek nextflow run nf core/sarek r 3.7.1 profile test,docker outdir test sarek atacseq nextflow run nf core/atacseq r 2.1.2 profile test,docker outdir test atacseq Verify: If test fails, see [references/troubleshooting.md](references/troubleshooting.md). Step 4: Create Samplesheet Generate automatically The script: Discovers FASTQ/BAM/CRAM files Pairs R1/R2 reads Infers sample metadata Validates before writing For sarek: Script prompts for tumor/normal status if not auto detected. Validate existing samplesheet Samplesheet formats rnaseq: sarek: atacseq: Step 5: Configure & Run 5a. Check genome availability Common genomes: GRCh38 (human), GRCh37 (legacy), GRCm39 (mouse), R64 1 1 (yeast), BDGP6 (fly) 5b. Decision points DECISION POINT: Confirm with user: 1. Genome: Which reference to use 2. Pipeline specific options: rnaseq: aligner (star salmon recommended, hisat2 for low memory) sarek: tools (haplotypecaller for germline, mutect2 for somatic) atacseq: read length (50, 75, 100, or 150) 5c. Run pipeline Key flags: r : Pin version profile docker : Use Docker (or singularity for HPC) genome : iGenomes key resume : Continue from checkpoint Resource limits (if needed): Step 6: Verify Outputs Check completion Key outputs by pipeline rnaseq: results/star salmon/salmon.merged.gene counts.tsv Gene counts results/star salmon/salmon.merged.gene tpm.tsv TPM values sarek: results/variant calling/ / VCF files results/preprocessing/recalibrated/ BAM files atacseq: results/macs2/narrowPeak/ Peak calls results/bwa/mergedLibrary/bigwig/ Coverage tracks Quick Reference For common exit codes and fixes, see [references/troubleshooting.md](references/troubleshooting.md). Resume failed run References [references/geo sra acquisition.md](references/geo sra acquisition.md) Downloading public GEO/SRA data [references/troubleshooting.md](references/troubleshooting.md) Common issues and fixes [references/installation.md](references/installation.md) Environment setup [references/pipelines/rnaseq.md](references/pipelines/rnaseq.md) RNA seq pipeline details [references/pipelines/sarek.md](references/pipelines/sarek.md) Variant calling details [references/pipelines/atacseq.md](references/pipelines/atacseq.md) ATAC seq details Disclaimer This skill is provided as a prototype example demonstrating how to integrate nf core bioinformatics pipelines into Claude Code for automated analysis workflows. The current implementation supports three pipelines (rnaseq, sarek, and atacseq), serving as a foundation that enables the community to expand support to the full set of nf core pipelines. It is intended for educational and research purposes and should not be considered production ready without appropriate validation for your specific use case. Users are responsible for ensuring their computing environment meets pipeline requirements and for verifying analysis results. Anthropic does not guarantee the accuracy of bioinformatics outputs, and users should follow standard practices for validating computational analyses. This integration is not officially endorsed by or affiliated with the nf core community. Attribution When publishing results, cite the appropriate pipeline. Citations are available in each nf core repository's CITATIONS.md file (e.g., https://github.com/nf core/rnaseq/blob/3.22.2/CITATIONS.md). Licenses nf core pipelines: MIT License (https://nf co.re/about) Nextflow: Apache License, Version 2.0 (https://www.nextflow.io/about us.html) NCBI SRA Toolkit: Public Domain (https://github.com/ncbi/sra tools/blob/master/LICENSE)

nextflow-development