opencode-knowledge-work 0.0.0-stage → 0.1.1

package/content/bio-research/skills/bio-research-nextflow-development/references/geo-sra-acquisition.md

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+# GEO/SRA Data Acquisition
+
+Download raw sequencing data from NCBI GEO/SRA and prepare it for nf-core pipelines.
+
+**Use this when:** Reanalyzing published datasets, validating findings, or comparing results against public cohorts.
+
+## Table of Contents
+
+- [Workflow Overview](#workflow-overview)
+- [Step 1: Fetch Study Information](#step-1-fetch-study-information)
+- [Step 2: Review Sample Groups](#step-2-review-sample-groups)
+- [Step 3: Download FASTQ Files](#step-3-download-fastq-files)
+- [Step 4: Generate Samplesheet](#step-4-generate-samplesheet)
+- [Step 5: Run nf-core Pipeline](#step-5-run-nf-core-pipeline)
+- [Supported Pipelines](#supported-pipelines)
+- [Supported Organisms](#supported-organisms)
+- [Complete Example](#complete-example)
+- [Troubleshooting](#troubleshooting)
+
+---
+
+## Workflow Overview
+
+Example: "Find differentially expressed genes in GSE309891 (drug-treated vs control)"
+
+```
+┌─────────────────────────────────────────────────────────────────┐
+│                    GEO/SRA DATA ACQUISITION                     │
+└─────────────────────────────────────────────────────────────────┘
+                              │
+                              ▼
+                 ┌────────────────────────┐
+                 │   Fetch study info     │
+                 │   • Query NCBI/SRA     │
+                 │   • Get metadata       │
+                 │   • Detect organism    │
+                 │   • Identify data type │
+                 └────────────────────────┘
+                              │
+                              ▼
+                 ┌────────────────────────┐
+                 │   Present summary      │
+                 │   • Organism: Human    │
+                 │   • Genome: GRCh38     │
+                 │   • Type: RNA-Seq      │
+                 │   • Pipeline: rnaseq   │
+                 │   • Samples: 12        │
+                 │     (6 treated,        │
+                 │      6 control)        │
+                 │   • Size: ~24 GB       │
+                 └────────────────────────┘
+                              │
+                              ▼
+                    ┌─────────────────┐
+                    │  USER CONFIRMS  │◄──── Decision point
+                    │  genome/pipeline│
+                    └─────────────────┘
+                              │
+                              ▼
+                 ┌────────────────────────┐
+                 │   Select samples       │
+                 │   • Group by condition │
+                 │   • Show treated/ctrl  │
+                 └────────────────────────┘
+                              │
+                              ▼
+                    ┌─────────────────┐
+                    │  USER SELECTS   │◄──── Decision point
+                    │  sample subset  │
+                    └─────────────────┘
+                              │
+                              ▼
+                 ┌────────────────────────┐
+                 │   Download FASTQs      │
+                 │   • 24 files (R1+R2)   │
+                 │   • Parallel transfers │
+                 │   • Auto-resume        │
+                 └────────────────────────┘
+                              │
+                              ▼
+                 ┌────────────────────────┐
+                 │   Generate samplesheet │
+                 │   • Map SRR to files   │
+                 │   • Pair R1/R2         │
+                 │   • Assign conditions  │
+                 └────────────────────────┘
+                              │
+                              ▼
+┌─────────────────────────────────────────────────────────────────┐
+│                    NF-CORE PIPELINE EXECUTION                   │
+│              (Continue with Step 1 of main workflow)            │
+└─────────────────────────────────────────────────────────────────┘
+```
+
+---
+
+## Instructions for Claude
+
+When assisting users with GEO/SRA data acquisition:
+
+1. **Always fetch study info first** to show the user what data is available
+2. **Ask for confirmation before downloading** - Present the sample groups and sizes, then ask which subset to download using AskUserQuestion
+3. **Suggest appropriate genome and pipeline** based on the organism and data type
+4. **Return to main SKILL.md workflow** after data preparation is complete
+
+Example confirmation question:
+```
+Question: "Which sample group would you like to download?"
+Options:
+  - "RNA-Seq:PAIRED (42 samples, ~87 GB)"
+  - "RNA-Seq:SINGLE (7 samples, ~4.5 GB)"
+  - "All samples (49 samples, ~92 GB)"
+```
+
+---
+
+## Step 1: Fetch Study Information
+
+Get metadata about a GEO study before downloading.
+
+```bash
+python scripts/sra_geo_fetch.py info <GEO_ID>
+```
+
+**Example:**
+```bash
+python scripts/sra_geo_fetch.py info GSE110004
+```
+
+**Output includes:**
+- Study title and summary
+- Organism (with auto-suggested genome)
+- Number of samples and runs
+- Data types (RNA-Seq, ATAC-seq, etc.)
+- Estimated download size
+- Suggested nf-core pipeline
+
+**Save info to JSON:**
+```bash
+python scripts/sra_geo_fetch.py info GSE110004 -o study_info.json
+```
+
+---
+
+## Step 2: Review Sample Groups
+
+View sample groups organized by data type and layout. This is useful for studies with mixed data types.
+
+```bash
+python scripts/sra_geo_fetch.py groups <GEO_ID>
+```
+
+**Example output:**
+```
+Sample Group          Count Layout     GSM Range                    Est. Size
+--------------------------------------------------------------------------------
+RNA-Seq                  42 PAIRED     GSM2879618...(42 samples)      87.4 GB
+RNA-Seq                   7 SINGLE     GSM2976181-GSM2976187           4.5 GB
+--------------------------------------------------------------------------------
+TOTAL                    49                                           91.9 GB
+
+Available groups for --subset option:
+  1. "RNA-Seq:PAIRED" - 42 samples (~87.4 GB)
+  2. "RNA-Seq:SINGLE" - 7 samples (~4.5 GB)
+```
+
+**List individual runs:**
+```bash
+python scripts/sra_geo_fetch.py list <GEO_ID>
+
+# Filter by data type
+python scripts/sra_geo_fetch.py list GSE110004 --filter "RNA-Seq:PAIRED"
+```
+
+**DECISION POINT:** Review the sample groups. Decide which subset to download if the study has multiple data types.
+
+---
+
+## Step 3: Download FASTQ Files
+
+Download FASTQ files from ENA (faster than SRA).
+
+```bash
+python scripts/sra_geo_fetch.py download <GEO_ID> -o <OUTPUT_DIR>
+```
+
+**Options:**
+- `-o, --output`: Output directory (required)
+- `-i, --interactive`: Interactively select sample group to download
+- `-s, --subset`: Filter by data type (e.g., "RNA-Seq:PAIRED")
+- `-p, --parallel`: Parallel downloads (default: 4)
+- `-t, --timeout`: Download timeout in seconds (default: 600)
+
+### Interactive Mode (Recommended)
+
+Use `-i` flag for interactive sample selection when the study has multiple data types:
+
+```bash
+python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i
+```
+
+**Interactive output:**
+```
+============================================================
+  SELECT SAMPLE GROUP TO DOWNLOAD
+============================================================
+
+  [1] RNA-Seq (paired)
+      Samples: 42
+      GSM: GSM2879618...(42 samples)
+      Size: ~87.4 GB
+
+  [2] RNA-Seq (single)
+      Samples: 7
+      GSM: GSM2976181-GSM2976187
+      Size: ~4.5 GB
+
+  [0] Download ALL (49 samples)
+------------------------------------------------------------
+
+Enter selection (0-2):
+```
+
+### Direct Subset Selection
+
+Alternatively, specify the subset directly:
+
+```bash
+# Download only RNA-Seq paired-end data
+python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq \
+    --subset "RNA-Seq:PAIRED" --parallel 6
+```
+
+**Note:** Downloads automatically skip existing files. Resume interrupted downloads by re-running the command.
+
+---
+
+## Step 4: Generate Samplesheet
+
+Create a samplesheet compatible with nf-core pipelines.
+
+```bash
+python scripts/sra_geo_fetch.py samplesheet <GEO_ID> \
+    --fastq-dir <FASTQ_DIR> \
+    -o samplesheet.csv
+```
+
+**Options:**
+- `-f, --fastq-dir`: Directory containing downloaded FASTQ files (required)
+- `-o, --output`: Output samplesheet path (default: samplesheet.csv)
+- `-p, --pipeline`: Target pipeline (auto-detected if not specified)
+
+**Example:**
+```bash
+python scripts/sra_geo_fetch.py samplesheet GSE110004 \
+    --fastq-dir ./fastq \
+    -o samplesheet.csv
+```
+
+**Output:** The script will:
+1. Create samplesheet in the format required by the target pipeline
+2. Display suggested genome reference
+3. Show suggested nf-core command
+
+---
+
+## Step 5: Run nf-core Pipeline
+
+After generating the samplesheet, the script provides a suggested command.
+
+**Example output:**
+```
+Suggested command:
+   nextflow run nf-core/rnaseq \
+       --input samplesheet.csv \
+       --outdir results \
+       --genome R64-1-1 \
+       -profile docker
+```
+
+**DECISION POINT:** Review and confirm:
+1. Is the suggested pipeline correct?
+2. Is the genome reference correct for your organism?
+3. Do you need additional pipeline options?
+
+Then return to the main SKILL.md workflow (Step 1: Environment Check) to proceed with pipeline execution.
+
+---
+
+## Supported Pipelines
+
+The skill auto-detects appropriate pipelines based on library strategy. Pipelines marked with ★ are fully supported with configs, samplesheet generation, and documentation. Others are suggested but require manual setup following nf-core documentation.
+
+| Library Strategy | Suggested Pipeline | Support |
+|------------------|--------------------|---------|
+| RNA-Seq          | nf-core/rnaseq     | ★ Full  |
+| ATAC-seq         | nf-core/atacseq    | ★ Full  |
+| WGS/WXS          | nf-core/sarek      | ★ Full  |
+| ChIP-seq         | nf-core/chipseq    | Manual  |
+| Bisulfite-Seq    | nf-core/methylseq  | Manual  |
+| miRNA-Seq        | nf-core/smrnaseq   | Manual  |
+| Amplicon         | nf-core/ampliseq   | Manual  |
+
+---
+
+## Supported Organisms
+
+Common organisms with auto-suggested genomes:
+
+| Organism | Genome | Notes |
+|----------|--------|-------|
+| Homo sapiens | GRCh38 | Human reference |
+| Mus musculus | GRCm39 | Mouse reference |
+| Saccharomyces cerevisiae | R64-1-1 | Yeast S288C |
+| Drosophila melanogaster | BDGP6 | Fruit fly |
+| Caenorhabditis elegans | WBcel235 | C. elegans |
+| Danio rerio | GRCz11 | Zebrafish |
+| Arabidopsis thaliana | TAIR10 | Arabidopsis |
+| Rattus norvegicus | Rnor_6.0 | Rat |
+
+See `scripts/config/genomes.yaml` for the full list.
+
+---
+
+## Complete Example
+
+Reanalyze GSE110004 (yeast RNA-seq):
+
+```bash
+# 1. Get study info and sample groups
+python scripts/sra_geo_fetch.py info GSE110004
+
+# 2. Download with interactive selection
+python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i
+# Select option [1] for RNA-Seq paired-end samples
+
+# 3. Generate samplesheet
+python scripts/sra_geo_fetch.py samplesheet GSE110004 \
+    --fastq-dir ./fastq \
+    -o samplesheet.csv
+
+# 4. Run nf-core/rnaseq (continue with main SKILL.md workflow)
+nextflow run nf-core/rnaseq \
+    --input samplesheet.csv \
+    --outdir results \
+    --genome R64-1-1 \
+    -profile docker
+```
+
+### Alternative: Non-interactive Download
+
+```bash
+# Review sample groups first
+python scripts/sra_geo_fetch.py groups GSE110004
+
+# Download specific subset directly
+python scripts/sra_geo_fetch.py download GSE110004 \
+    --subset "RNA-Seq:PAIRED" \
+    -o ./fastq \
+    --parallel 4
+```
+
+---
+
+## Troubleshooting
+
+### ENA Download Fails
+If ENA downloads fail, the data may need to be fetched directly from SRA:
+
+```bash
+# Create SRA tools environment
+conda create -n sra_tools -c bioconda sra-tools
+
+# Download with prefetch + fasterq-dump
+conda run -n sra_tools prefetch SRR6357070
+conda run -n sra_tools fasterq-dump SRR6357070 -O ./fastq
+```
+
+### No SRA Runs Found
+Some GEO datasets only have processed data, not raw sequencing reads. Check:
+```bash
+python scripts/sra_geo_fetch.py info <GEO_ID>
+```
+If "Runs: 0", the dataset may not have raw data in SRA.
+
+### SuperSeries Support
+GEO SuperSeries (which contain multiple SubSeries) are automatically handled. The tool will:
+1. Detect that a GEO ID is a SuperSeries
+2. Find the linked BioProject accession
+3. Fetch all SRA runs from the BioProject
+
+Example: GSE110004 is a SuperSeries that links to BioProject PRJNA432544.
+
+### Genome Not Recognized
+If the organism is not in the genome mapping, manually specify the genome:
+```bash
+# Check available iGenomes
+python scripts/manage_genomes.py list
+
+# Or provide custom reference files to nf-core
+nextflow run nf-core/rnaseq --fasta /path/to/genome.fa --gtf /path/to/genes.gtf
+```
+
+---
+
+## Requirements
+
+- Python 3.8+
+- `requests` library (optional but recommended)
+- `pyyaml` library (optional, for genome config)
+- Network access to NCBI and ENA
+
+Install optional dependencies:
+```bash
+pip install requests pyyaml
+```

package/content/bio-research/skills/bio-research-nextflow-development/references/installation.md

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+# Installation
+
+## Contents
+- [Quick install](#quick-install)
+- [Docker setup](#docker-setup)
+- [Singularity setup (HPC)](#singularity-setup-hpc)
+- [nf-core tools (optional)](#nf-core-tools-optional)
+- [Verify installation](#verify-installation)
+- [Common issues](#common-issues)
+
+## Quick install
+
+```bash
+# Nextflow
+curl -s https://get.nextflow.io | bash
+mv nextflow ~/bin/
+export PATH="$HOME/bin:$PATH"
+
+# Verify
+nextflow -version
+java -version  # Requires 11+
+```
+
+## Docker setup
+
+### Linux
+```bash
+sudo apt-get update && sudo apt-get install docker.io
+sudo systemctl enable --now docker
+sudo usermod -aG docker $USER
+# Log out and back in
+```
+
+### macOS
+Download Docker Desktop: https://docker.com/products/docker-desktop
+
+### Verify
+```bash
+docker run hello-world
+```
+
+## Singularity setup (HPC)
+
+```bash
+# Ubuntu/Debian
+sudo apt-get install singularity-container
+
+# Or via conda
+conda install -c conda-forge singularity
+```
+
+### Configure cache
+```bash
+export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"
+mkdir -p $NXF_SINGULARITY_CACHEDIR
+echo 'export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"' >> ~/.bashrc
+```
+
+## nf-core tools (optional)
+
+```bash
+pip install nf-core
+```
+
+Useful commands:
+```bash
+nf-core list                    # Available pipelines
+nf-core launch rnaseq           # Interactive parameter selection
+nf-core download rnaseq -r 3.14.0  # Download for offline use
+```
+
+## Verify installation
+
+```bash
+nextflow run nf-core/demo -profile test,docker --outdir test_demo
+ls test_demo/
+```
+
+## Common issues
+
+**Java version wrong:**
+```bash
+export JAVA_HOME=/path/to/java11
+```
+
+**Docker permission denied:**
+```bash
+sudo usermod -aG docker $USER
+# Log out and back in
+```
+
+**Nextflow not found:**
+```bash
+echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc
+source ~/.bashrc
+```

package/content/bio-research/skills/bio-research-nextflow-development/references/pipelines/atacseq.md

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+# nf-core/atacseq
+
+**Version:** 2.1.2
+
+**Official Documentation:** https://nf-co.re/atacseq/2.1.2/
+**GitHub:** https://github.com/nf-core/atacseq
+
+> **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/atacseq/releases) for breaking changes and update the version in commands below.
+
+## Contents
+- [Test command](#test-command)
+- [Samplesheet format](#samplesheet-format)
+- [Parameters](#parameters)
+- [Output files](#output-files)
+- [Quality metrics](#quality-metrics)
+
+## Test command
+
+```bash
+nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq
+```
+
+Expected: ~15 min, creates peaks and BigWig tracks.
+
+## Samplesheet format
+
+```csv
+sample,fastq_1,fastq_2,replicate
+CONTROL,/path/to/ctrl_rep1_R1.fq.gz,/path/to/ctrl_rep1_R2.fq.gz,1
+CONTROL,/path/to/ctrl_rep2_R1.fq.gz,/path/to/ctrl_rep2_R2.fq.gz,2
+TREATMENT,/path/to/treat_rep1_R1.fq.gz,/path/to/treat_rep1_R2.fq.gz,1
+TREATMENT,/path/to/treat_rep2_R1.fq.gz,/path/to/treat_rep2_R2.fq.gz,2
+```
+
+| Column | Required | Description |
+|--------|----------|-------------|
+| sample | Yes | Condition/group identifier |
+| fastq_1 | Yes | Absolute path to R1 |
+| fastq_2 | Yes | Absolute path to R2 (paired-end required) |
+| replicate | Yes | Replicate number (integer) |
+
+### Design file for differential analysis
+```csv
+sample,condition
+CONTROL,control
+TREATMENT,treatment
+```
+
+Use with `--deseq2_design design.csv`.
+
+## Parameters
+
+### Minimal run
+```bash
+nextflow run nf-core/atacseq -r 2.1.2 -profile docker \
+    --input samplesheet.csv --outdir results --genome GRCh38 --read_length 50
+```
+
+### Common parameters
+
+| Parameter | Default | Description |
+|-----------|---------|-------------|
+| `--genome` | - | `GRCh38`, `GRCh37`, `mm10` |
+| `--read_length` | 50 | Read length for MACS2 optimization |
+| `--narrow_peak` | true | Narrow peaks (false for broad) |
+| `--mito_name` | chrM | Mitochondrial chromosome name |
+| `--keep_mito` | false | Keep mitochondrial reads |
+| `--min_reps_consensus` | 1 | Min replicates for consensus peaks |
+
+### Differential accessibility
+```bash
+--deseq2_design design.csv
+```
+
+## Output files
+
+```
+results/
+├── bwa/mergedLibrary/
+│   ├── *.mLb.mkD.sorted.bam     # Filtered, deduplicated alignments
+│   └── bigwig/
+│       └── *.bigWig             # Coverage tracks
+├── macs2/narrowPeak/
+│   ├── *.narrowPeak             # Peak calls
+│   └── consensus/
+│       └── consensus_peaks.bed  # Merged peaks across replicates
+├── deeptools/
+│   ├── plotFingerprint/         # Library complexity
+│   └── plotProfile/             # TSS enrichment
+├── deseq2/                      # If --deseq2_design provided
+└── multiqc/
+```
+
+**Key outputs:**
+- `*.mLb.mkD.sorted.bam`: Analysis-ready alignments
+- `*.narrowPeak`: MACS2 peak calls (BED format)
+- `consensus_peaks.bed`: Consensus peaks across replicates
+- `*.bigWig`: Genome browser tracks
+
+## Quality metrics
+
+| Metric | Good | Acceptable | Poor |
+|--------|------|------------|------|
+| Mapped reads | >80% | 60-80% | <60% |
+| Mitochondrial | <20% | 20-40% | >40% |
+| Duplicates | <30% | 30-50% | >50% |
+| FRiP | >30% | 15-30% | <15% |
+| TSS enrichment | >6 | 4-6 | <4 |
+
+**Fragment size**: Should show nucleosomal periodicity (~50bp nucleosome-free, ~200bp mono-nucleosome).
+
+## Downstream analysis
+
+```r
+library(ChIPseeker)
+library(GenomicRanges)
+peaks <- import("consensus_peaks.bed")
+peakAnno <- annotatePeak(peaks, TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene)
+```
+
+**Motif analysis:**
+```bash
+findMotifsGenome.pl consensus_peaks.bed hg38 motifs/ -size 200
+```
+
+## Troubleshooting
+
+**Low FRiP**: Check library complexity in `plotFingerprint/`. May indicate over-transposition.
+
+**Few peaks**: Lower threshold with `--macs_qvalue 0.1` or use `--narrow_peak false` for broader peaks.
+
+**High duplicates**: Normal for low-input; pipeline removes by default.
+
+## More Information
+
+- **Full parameter list:** https://nf-co.re/atacseq/2.1.2/parameters/
+- **Output documentation:** https://nf-co.re/atacseq/2.1.2/docs/output/
+- **Usage documentation:** https://nf-co.re/atacseq/2.1.2/docs/usage/