nextflow-developmentlisted

# 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](references/geo-sra-acquisition.md) for the full workflow. **Quick start:** ```bash # 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.** ``