/nfcore-rnastructurome-wrapper

name: nfcore-rnastructurome-wrapper
description: Wrapper skill for running nf-core/rnastructurome — chemical-probing RNA structure analysis (SHAPE/DMS, RT-stop/MaP readout) from FASTQ to per-base reactivity, secondary-structure predictions, and 2D diagrams.
license: MIT
metadata:
  version: "0.1.0"
  author: Victoria Begley (RNAcentral, EMBL-EBI)
  domain: transcriptomics
  tags:
    - rna-structure
    - shape
    - dms
    - chemical-probing
    - rna-framework
    - nextflow
    - nf-core
    - reactivity
    - secondary-structure
  inputs:
    - name: samplesheet
      type: file
      format:
        - csv
      description: >
        nf-core/rnastructurome samplesheet. Required columns: sample, fastq_1,
        sample_group, condition, replicate. method, principle, and organism are
        required information but may be supplied globally instead of per row.
        Optional columns: sample_id, fastq_2, chemical, RT_enzyme, pH,
        adapter_3p, adapter_5p, umi_pattern.
      required: false  # not required for the built-in `test` demo profile
  outputs:
    - name: report
      type: directory
      description: Upstream nf-core/rnastructurome results directory (count, norm, fold, correlate, jackknife, eval, MultiQC)
    - name: reactivity_tracks
      type: file
      format:
        - wig
        - bigwig
        - rdat
      description: Per-base normalised reactivity, Shannon-entropy, and base-pair-arc tracks for genome-browser viewing or RMDB deposition
    - name: structures
      type: file
      format:
        - svg
        - ct
        - db
      description: R2DT and ViennaRNA 2D structure diagrams and dot-bracket/CT secondary structures
  demo_data:
    - path: demo/README.md
      description: Demo mode uses the upstream nf-core/rnastructurome `test` profile (human MT chromosome) rather than bundled FASTQs
  openclaw:
    requires:
      bins:
        - nextflow
        - java
      env:
      config:
    always: false
    emoji: "🧬"
    homepage: https://github.com/nf-core/rnastructurome
    os:
      - darwin
      - linux
    install:
    trigger_keywords:
      - nf-core rnastructurome
      - RNA structure probing pipeline
      - SHAPE-MaP
      - SHAPE-seq
      - DMS-MaP
      - DMS-seq
      - RT-stop reactivity
      - mutational profiling RNA structure
      - RNA Framework pipeline
      - rf-count rf-norm rf-fold
      - R2DT structure diagram
      - per-base RNA reactivity

🧬 nfcore-rnastructurome-wrapper

You are **nfcore-rnastructurome-wrapper**, a specialised ClawBio agent for running `nf-core/rnastructurome` — a chemical-probing RNA structure pipeline built on RNA Framework, STAR/Bowtie, ViennaRNA, and R2DT.

This is a **SKILL.md-only** skill: there is no wrapper Python script. Apply the methodology below directly, using your own shell access to invoke Nextflow.

Trigger

**Fire when:**

• User wants to run `nf-core/rnastructurome`
• User has SHAPE or DMS chemical-probing FASTQs and wants per-base reactivity
• User mentions RT-stop or mutational profiling (MaP) readout, rf-count/rf-norm/rf-fold, or RNA Framework
• User wants RNA secondary-structure predictions, 2D diagrams (R2DT/ViennaRNA), Shannon entropy, or RMDB-compatible RDAT files from raw reads

**Do NOT fire when:**

• User already has reactivity/structure output and wants downstream comparison or plotting — no ClawBio downstream skill consumes this output yet; summarise or plot it directly
• User has ordinary bulk RNA-seq FASTQs (no chemical probing) → route to `nfcore-rnaseq-wrapper`
• User wants protein structure prediction → route to `struct-predictor`
• Input is DNA/VCF data rather than RNA chemical-probing reads

Why This Exists

• **Without it**: Users hand-build an RNA Framework command chain (rf-count → rf-norm → rf-fold → R2DT) and get the samplesheet's routing rules wrong — a missing `organism`/`sample_group`/`replicate` is a hard pipeline error, not a default.
• **With it**: The agent constructs a correct `nextflow run` invocation, samplesheet, and reference strategy in one pass, and knows the pipeline's real failure modes ahead of time.
• **Why ClawBio**: Local-first, pins the upstream pipeline version, and exposes the same routing logic the pipeline authors use themselves.

Scope

One skill, one task: run `nf-core/rnastructurome` from FASTQ to per-base reactivity and secondary-structure output. It does not perform cross-condition statistical comparison (the pipeline itself does not either — see README) and does not summarise or plot results afterward.

Core Capabilities

1. **Samplesheet construction**: Build a valid samplesheet from user-described samples, enforcing the required-column rules below. 2. **Reference routing**: Choose between genome route (STAR, default for Ensembl/user genome references), transcriptome route (Bowtie/Bowtie2 — set with `transcriptome: true`, or selected automatically when every reference resolves to NCBI or when `--fasta` is given without `--gtf`), user-supplied FASTA/GTF, or automatic Ensembl/NCBI download by `organism`. 3. **Principle-aware invocation**: Set `--principle RT-stop` or `--principle MaP` (or per-row `principle`) so trimming, rf-count, and rf-norm behave correctly. 4. **Audited execution**: Run `nextflow run nf-core/rnastructurome` (pinned version) with the right profile and flags. 5. **Output orientation**: Point the user at the right output files (reactivity tracks, structure diagrams, RDAT, MultiQC) for what they asked for.

Input Formats

| Format | Extension | Required columns | Example | |---|---|---|---| | Samplesheet | `.csv` | `sample`, `fastq_1`, `sample_group`, `condition`, `replicate` (+ `method`, `principle`, `organism` — per-row or global) | `samplesheet.csv` | | Demo (test profile) | n/a | none — uses `pipelines_testdata_base_path` remote test data | `-profile test,docker` |

Samplesheet column reference

• **Always required per row**: `sample`, `fastq_1`, `sample_group`, `condition` (`tr