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 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

Nextflow issues

Java issues

Do not proceed until all checks pass. For HPC/Singularity, see references/troubleshooting.md.

Step 2: Select Pipeline

DECISION POINT: Confirm with user before proceeding.

Auto-detect from data:

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

For pipeline-specific details:

• references/pipelines/rnaseq.md
• references/pipelines/sarek.md
• references/pipelines/atacseq.md

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

Verify:

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

If test fails, see references/troubleshooting.md.

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

…