Bio Research

Skill 2 of 200

Nextflow Development

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data.

3 minutes · 627 words · 26 sections

Install

$ npx skills add anthropics/knowledge-work-plugins --skill nextflow-development

$ npx skills add anthropics/knowledge-work-plugins

» /plugin marketplace add anthropics/knowledge-work-plugins

The first command installs just this skill, by the name in its SKILL.md; the second installs the whole repository.

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)
- [ ] 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

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 (opens in a new tab) for the full workflow.

Quick start:

# 1. Get study info
python scripts/sra_geo_fetch.py info GSE110004

# 2. Download (interactive mode)
python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i

# 3. Generate samplesheet
python scripts/sra_geo_fetch.py samplesheet GSE110004 --fastq-dir ./fastq -o samplesheet.csv

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.

python scripts/check_environment.py

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/ (opens in a new tab)
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 (opens in a new tab).

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:

python scripts/detect_data_type.py /path/to/data

For pipeline-specific details:

Step 3: Run Test Profile

Validates environment with small data. MUST pass before real data.

nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output

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:

ls test_output/multiqc/multiqc_report.html
grep "Pipeline completed successfully" .nextflow.log

If test fails, see references/troubleshooting.md (opens in a new tab).

Step 4: Create Samplesheet

Generate automatically

python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv

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

python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>

Samplesheet formats

rnaseq:

sample,fastq_1,fastq_2,strandedness
SAMPLE1,/abs/path/R1.fq.gz,/abs/path/R2.fq.gz,auto

sarek:

patient,sample,lane,fastq_1,fastq_2,status
patient1,tumor,L001,/abs/path/tumor_R1.fq.gz,/abs/path/tumor_R2.fq.gz,1
patient1,normal,L001,/abs/path/normal_R1.fq.gz,/abs/path/normal_R2.fq.gz,0

atacseq:

sample,fastq_1,fastq_2,replicate
CONTROL,/abs/path/ctrl_R1.fq.gz,/abs/path/ctrl_R2.fq.gz,1

Step 5: Configure & Run

5a. Check genome availability

python scripts/manage_genomes.py check <genome>
# If not installed:
python scripts/manage_genomes.py download <genome>

Common genomes: GRCh38 (human), GRCh37 (legacy), GRCm39 (mouse), R64-1-1 (yeast), BDGP6 (fly)

5b. Decision points

DECISION POINT: Confirm with user:

Genome: Which reference to use
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

nextflow run nf-core/<pipeline> \
    -r <version> \
    -profile docker \
    --input samplesheet.csv \
    --outdir results \
    --genome <genome> \
    -resume

Key flags:

-r: Pin version
-profile docker: Use Docker (or singularity for HPC)
--genome: iGenomes key
-resume: Continue from checkpoint

Resource limits (if needed):

--max_cpus 8 --max_memory '32.GB' --max_time '24.h'

Step 6: Verify Outputs

Check completion

ls results/multiqc/multiqc_report.html
grep "Pipeline completed successfully" .nextflow.log

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 (opens in a new tab).

Resume failed run

nextflow run nf-core/<pipeline> -resume

References

references/geo-sra-acquisition.md (opens in a new tab) - Downloading public GEO/SRA data
references/troubleshooting.md (opens in a new tab) - Common issues and fixes
references/installation.md (opens in a new tab) - Environment setup
references/pipelines/rnaseq.md (opens in a new tab) - RNA-seq pipeline details
references/pipelines/sarek.md (opens in a new tab) - Variant calling details
references/pipelines/atacseq.md (opens in a new tab) - 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 (opens in a new tab)).

Licenses

nf-core pipelines: MIT License (https://nf-co.re/about (opens in a new tab))
Nextflow: Apache License, Version 2.0 (https://www.nextflow.io/about-us.html (opens in a new tab))
NCBI SRA Toolkit: Public Domain (https://github.com/ncbi/sra-tools/blob/master/LICENSE (opens in a new tab))

About this skill

Trigger

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.

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How this issue was made

Source

github.com/anthropics/knowledge-work-plugins, branch main, last pushed 23 September 2026.

Licence

Apache-2.0 — the text of every skill is reproduced unmodified, frontmatter included, under the upstream licence.

Discovery

200 skills found by walking the repository tree for SKILL.md, not by matching a directory convention. 27 distinct layouts observed: bio-research/skills/*/SKILL.md, cowork-plugin-management/skills/*/SKILL.md, customer-support/skills/*/SKILL.md, data/skills/*/SKILL.md, design/skills/*/SKILL.md, engineering/skills/*/SKILL.md, enterprise-search/skills/*/SKILL.md, finance/skills/*/SKILL.md, human-resources/skills/*/SKILL.md, legal/skills/*/SKILL.md, marketing/skills/*/SKILL.md, operations/skills/*/SKILL.md, partner-built/apollo/skills/*/SKILL.md, partner-built/brand-voice/skills/*/SKILL.md, partner-built/common-room/skills/*/SKILL.md, partner-built/slack/skills/*/SKILL.md, partner-built/zoom-plugin/skills/*/SKILL.md, partner-built/zoom-plugin/skills/contact-center/*/SKILL.md, partner-built/zoom-plugin/skills/meeting-sdk/*/SKILL.md, partner-built/zoom-plugin/skills/meeting-sdk/web/*/SKILL.md, partner-built/zoom-plugin/skills/video-sdk/*/SKILL.md, partner-built/zoom-plugin/skills/virtual-agent/*/SKILL.md, partner-built/zoom-plugin/skills/zoom-mcp/*/SKILL.md, pdf-viewer/skills/*/SKILL.md, product-management/skills/*/SKILL.md, productivity/skills/*/SKILL.md, sales/skills/*/SKILL.md.

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nf-core Pipeline Deployment

Run nf-core bioinformatics pipelines on local or public sequencing data.

Workflow Checklist

- [ ] 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

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 (opens in a new tab) for the full workflow.

Quick start:

# 1. Get study info
python scripts/sra_geo_fetch.py info GSE110004

# 2. Download (interactive mode)
python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i

# 3. Generate samplesheet
python scripts/sra_geo_fetch.py samplesheet GSE110004 --fastq-dir ./fastq -o samplesheet.csv

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.

python scripts/check_environment.py

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/ (opens in a new tab)
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 (opens in a new tab).

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:

python scripts/detect_data_type.py /path/to/data

For pipeline-specific details:

Step 3: Run Test Profile

Validates environment with small data. MUST pass before real data.

nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output

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:

ls test_output/multiqc/multiqc_report.html
grep "Pipeline completed successfully" .nextflow.log

If test fails, see references/troubleshooting.md (opens in a new tab).

Step 4: Create Samplesheet

Generate automatically

python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv

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

python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>

Samplesheet formats

rnaseq:

sample,fastq_1,fastq_2,strandedness
SAMPLE1,/abs/path/R1.fq.gz,/abs/path/R2.fq.gz,auto

sarek:

patient,sample,lane,fastq_1,fastq_2,status
patient1,tumor,L001,/abs/path/tumor_R1.fq.gz,/abs/path/tumor_R2.fq.gz,1
patient1,normal,L001,/abs/path/normal_R1.fq.gz,/abs/path/normal_R2.fq.gz,0

atacseq:

sample,fastq_1,fastq_2,replicate
CONTROL,/abs/path/ctrl_R1.fq.gz,/abs/path/ctrl_R2.fq.gz,1

Step 5: Configure & Run

5a. Check genome availability

python scripts/manage_genomes.py check <genome>
# If not installed:
python scripts/manage_genomes.py download <genome>

Common genomes: GRCh38 (human), GRCh37 (legacy), GRCm39 (mouse), R64-1-1 (yeast), BDGP6 (fly)

5b. Decision points

DECISION POINT: Confirm with user:

Genome: Which reference to use
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

nextflow run nf-core/<pipeline> \
    -r <version> \
    -profile docker \
    --input samplesheet.csv \
    --outdir results \
    --genome <genome> \
    -resume

Key flags:

-r: Pin version
-profile docker: Use Docker (or singularity for HPC)
--genome: iGenomes key
-resume: Continue from checkpoint

Resource limits (if needed):

--max_cpus 8 --max_memory '32.GB' --max_time '24.h'

Step 6: Verify Outputs

Check completion

ls results/multiqc/multiqc_report.html
grep "Pipeline completed successfully" .nextflow.log

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 (opens in a new tab).

Resume failed run

nextflow run nf-core/<pipeline> -resume

References

references/geo-sra-acquisition.md (opens in a new tab) - Downloading public GEO/SRA data
references/troubleshooting.md (opens in a new tab) - Common issues and fixes
references/installation.md (opens in a new tab) - Environment setup
references/pipelines/rnaseq.md (opens in a new tab) - RNA-seq pipeline details
references/pipelines/sarek.md (opens in a new tab) - Variant calling details
references/pipelines/atacseq.md (opens in a new tab) - ATAC-seq details

nf-core pipelines: MIT License (https://nf-co.re/about (opens in a new tab))
Nextflow: Apache License, Version 2.0 (https://www.nextflow.io/about-us.html (opens in a new tab))
NCBI SRA Toolkit: Public Domain (https://github.com/ncbi/sra-tools/blob/master/LICENSE (opens in a new tab))

About this skill

Trigger

Colophon

Appendix 2.1–2.21

ReferencesMarkdown · 6 files

Scripts14 files

Also bundledText · 1 file

About this skill

Trigger

Colophon

Appendix 2.1–2.21

ReferencesMarkdown · 6 files

Scripts14 files

Also bundledText · 1 file