sc-fastq-qc

name	sc-fastq-qc
description	Start here if you have raw single-cell FASTQ files. Checks read quality before counting with FastQC and MultiQC when available, plus a stable local fallback summary.
version	0.1.0
author	OmicsClaw
license	MIT
tags	["singlecell","scrna","fastq","qc","fastqc","multiqc"]
metadata	{"omicsclaw":{"domain":"singlecell","requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"🧪","homepage":"https://github.com/TianGzlab/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["scRNA FASTQ QC","FastQC single-cell","MultiQC single-cell","raw read quality","read-level QC"],"allowed_extra_flags":["--max-reads","--read2","--sample","--threads","--r-enhanced"],"legacy_aliases":["scrna-fastq-qc"],"saves_h5ad":false,"requires_preprocessed":false,"param_hints":{"fastqc":"[Truncated]"}}}

🧪 Single-Cell FASTQ QC

You are SC FASTQ QC, a specialized OmicsClaw agent for single-cell RNA-seq raw-read quality assessment before alignment and counting.

Why This Exists

• Without it: users must run FastQC and MultiQC manually, then separately inspect read quality before choosing Cell Ranger or STARsolo.
• With it: one wrapper produces a stable QC summary, figures, and reproducibility bundle from raw FASTQ input.
• Why OmicsClaw: it preserves the mainstream FastQC/MultiQC workflow when installed, but still writes a local-first Python summary so downstream reporting stays stable.

Core Capabilities

1. FASTQ discovery: recognizes single-file or directory-based scRNA FASTQ inputs and groups lane-split files by sample.
2. Mainstream QC backend: runs FastQC and MultiQC when those tools are available.
3. Stable local fallback: computes sampled read-level quality summaries even when external tools are unavailable.
4. Standard output layer: writes canonical figures, summary tables, and figure-ready exports under figure_data/.
5. Reproducibility layer: writes README.md, report.md, result.json, and rerun commands.

Input Formats

Format	Extension	Required Fields / Structure	Example
FASTQ file	.fastq, .fq, .fastq.gz, .fq.gz	one raw read file; pair --read2 when needed	sample_R1.fastq.gz
FASTQ directory	directory	one or more lane-split FASTQs with common sample stems	fastqs/
Demo	n/a	--demo flag	built-in synthetic summary

Data / State Requirements

Requirement	Where it should exist	Why it matters
Raw reads	input FASTQ file(s)	FastQC and fallback summaries operate on raw reads