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Localized reading guide

nextflow-developmentPurpose, usage and source

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.

Source retrieved:

Source repository
anthropics/knowledge-work-plugins
SKILL.md
bio-research/skills/nextflow-development/SKILL.md
Repository stars
34,049
Repository updated
2026-10-30
Categories
research
Last collected

License: License file needs review

Source SKILL.md

Workflow excerpts are reading aids, not executable instructions from Codez. No third-party Skill was run to produce this page.

The purpose and workflow passages below are upstream material, organized and translated for reading. They are distinct from the separately labeled Codez editorial analysis.

What this Skill does

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.

How the upstream workflow works

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.

Upstream passage · L6 ↗

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 for the full workflow. DECISION POINT: After fetching study info, confirm with user: Which sample subset to download (if multiple data types)

Upstream passage · L26 ↗

Step 2: Select Pipeline

DECISION POINT: Confirm with user before proceeding. Auto-detect from data: For pipeline-specific details:

Upstream passage · L88 ↗
Upstream passage · ↗
- [ ] Step 0: Acquire data (if from GEO/SRA)
- [ ] Step 1: Environment check (MUST pass)
- [ ] Step 2: Select pipeline (confirm with user)
- [ ] Step 3: Run test profile (MUST pass)
- [ ] Step 4: Create samplesheet
- [ ] Step 5: Configure & run (confirm genome with user)
- [ ] Step 6: Verify outputs

Requirements and setup

Step 1: Environment Check

Run first. Pipeline will fail without passing environment. All critical checks must pass. If any fail, provide fix instructions:

Upstream passage · L53 ↗

Limits and quality checks

No separate limits passage was selected from this file. This does not mean the Skill is safe for every input or environment. Review the complete source and validate your own result.

Start with a safe trial

  1. Check the supported host and the repository installation instructions. Keep the Skill directory and its referenced scripts, assets and documentation together; SKILL.md alone may omit dependencies.
  2. Give the agent your real input, desired output and acceptance criteria. Invocation syntax and available tools depend on the host; this site does not assume a universal install command.
  3. Try the source workflow in a disposable project or on a copy. Review operations that change files, remote services or billable resources before allowing them.
  4. Validate the output against the source quality checks and your own requirements. A successful trigger or a high repository Star count does not establish a correct result.

Skill format and directory specification ↗

Read further in the source

Translation and scope

This reading guide selects passages from the pinned upstream SKILL.md. Translation is assisted. It is not a complete manual or a claim of tested compatibility. Read the original and its referenced files before use.

This introduction refers to the pinned version below; current repository activity and collection time are shown separately.

Source retrieved
Source commit
2574e29377c7173d0cecffef29a6ecbd7f8ccb5d
Source SHA-256
f30017df5d499427a701ec6cedfc5c9948ca3bd04ee1a2b6a585a29cd93ad0d7
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