Individual skill
nextflow-development
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 reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
skills-imported/nextflow-development/SKILL.md
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- Last checked
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- Repository last updated
- Oct 10, 2026
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- MIT
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CONNECTORS.mddoc · 1,409 bytesLICENSE.txtdoc · 10,254 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesSKILL.mdcore · 9,229 bytesreferences/geo-sra-acquisition.mddoc · 14,123 bytesreferences/installation.mddoc · 1,816 bytesreferences/pipelines/atacseq.mddoc · 4,181 bytesreferences/pipelines/rnaseq.mddoc · 3,614 bytesreferences/pipelines/sarek.mddoc · 4,018 bytesreferences/troubleshooting.mddoc · 3,368 bytesscripts/check_environment.pyruns · 14,111 bytesscripts/config/genomes.yamlasset · 3,520 bytesscripts/config/pipelines/atacseq.yamlasset · 5,158 bytesscripts/config/pipelines/rnaseq.yamlasset · 4,173 bytesscripts/config/pipelines/sarek.yamlasset · 6,278 bytesscripts/detect_data_type.pyruns · 9,953 bytesscripts/generate_samplesheet.pyruns · 15,440 bytesscripts/manage_genomes.pyruns · 16,718 bytesscripts/sra_geo_fetch.pyruns · 24,982 bytesscripts/utils/__init__.pyruns · 1,788 bytesscripts/utils/file_discovery.pyruns · 5,169 bytesscripts/utils/ncbi_utils.pyruns · 28,480 bytesscripts/utils/sample_inference.pyruns · 7,848 bytesscripts/utils/validators.pyruns · 8,419 bytes
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<!-- Provenance: adapted from anthropics/knowledge-work-plugins (Apache-2.0, (c) Anthropic).
Original skill: https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research/skills/nextflow-development. Changes for Muse AI: Claude/Cowork product refs -> Muse AI; MCP -> connector; CLAUDE.md -> MUSE.md; ${CLAUDE_PLUGIN_ROOT} -> this skill's directory; /plugin:command refs -> skill refs. -->
# 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 (if from GEO/SRA)