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运行 nf-core/Nextflow 流水线，完成 RNA-seq、变异检测与 ATAC-seq 数据分析
复制安装指令，让 AI 自动完成配置 · 推荐新手
请帮我安装 askskill 上的 "nextflow-development" 技能： 1. 下载 https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/bio-research/skills/nextflow-development/SKILL.md 2. 保存为 ~/.claude/skills/nextflow-development/SKILL.md 3. 装好后重载技能，告诉我可以用了
请用 nf-core/rnaseq 分析本地 FASTQ 数据，生成 samplesheet，并输出基因表达定量、质控结果和差异表达分析所需文件。
返回可运行的流程配置、samplesheet 结构说明，以及表达定量与质控产物清单。
请使用 nf-core/sarek 对 WGS/WES 测序数据进行变异检测，说明需要的输入格式、参考基因组配置和主要输出文件。
返回 Sarek 流程的运行方案，并列出 SNP/Indel/结构变异等关键结果文件。
我有 GEO/SRA 的 GSE、GSM 或 SRR 编号，请帮我整理下载与分析步骤，并选择合适的 nf-core 流水线完成复现分析。
返回从公开编号到样本表、下载流程和下游分析方案的完整执行建议。
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.
- [ ] 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
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.
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:
Then continue to Step 1.
Run first. Pipeline will fail without passing environment.
python scripts/check_environment.py
All critical checks must pass. If any fail, provide fix instructions:
| 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 |
| Problem | Fix |
|---|---|
| Not installed | curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ |
| Version < 23.04 | nextflow self-update |
| 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.
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:
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.
python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv
The script:
…
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