Research · Skill
nf-core Pipeline Deployment
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.
- Ships scripts Phở cannot run yet
What the skill covers
The sections of its instructions, in order.
- 01 Workflow Checklist
- 02 Step 0: Acquire Data (GEO/SRA Only)
- 03 Step 1: Environment Check
- Docker issues
- Nextflow issues
- Java issues
- 04 Step 2: Select Pipeline
- 05 Step 3: Run Test Profile
- 06 Step 4: Create Samplesheet
- Generate automatically
- Validate existing samplesheet
- Samplesheet formats
- 07 Step 5: Configure & Run
- 5a. Check genome availability
- 5b. Decision points
- 5c. Run pipeline
- 08 Step 6: Verify Outputs
- Check completion
- Key outputs by pipeline
- 09 Quick Reference
Reference files
20 files Phở can open while it uses the skill.
- references/geo-sra-acquisition.md
- references/installation.md
- references/pipelines/atacseq.md
- references/pipelines/rnaseq.md
- references/pipelines/sarek.md
- references/troubleshooting.md
- scripts/check_environment.py
- scripts/config/genomes.yaml
- scripts/config/pipelines/atacseq.yaml
- scripts/config/pipelines/rnaseq.yaml
- scripts/config/pipelines/sarek.yaml
- scripts/detect_data_type.py
- scripts/generate_samplesheet.py
- scripts/manage_genomes.py
- scripts/sra_geo_fetch.py
- scripts/utils/__init__.py
- +4 more
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Frequently asked questions
What does nf-core Pipeline Deployment do?
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.
Is nf-core Pipeline Deployment free to use?
Yes. nf-core Pipeline Deployment is published by Anthropic under the Apache 2.0 licence, and you can use it with a free Phở account.
How do I use nf-core Pipeline Deployment in Phở?
Press Open in Phở, then Try to apply it to your next message, or add the Bio research set so Phở loads it whenever a request matches.
Does nf-core Pipeline Deployment need other tools?
No. It works in a normal Phở chat with what you type or upload. It also ships scripts, which Phở chat cannot run yet; Phở follows its written steps.
Copied unchanged from anthropics/knowledge-work-plugins at commit d900840 and credited to Anthropic, who is not affiliated with Phở. The full instructions and licence text ship with the skill inside Phở.