rnaseq-qc

name	rnaseq-qc
description	Run quality control on bulk RNA-seq data — adapter trimming, FastQC, alignment-rate checks, and a per-sample QC summary table. Use when the user has raw FASTQ files and needs a QC pass before differential expression.
domains	["bioinfo","qc"]

RNA-seq QC

Quality-control workflow for bulk RNA-seq before differential expression.

Steps

1. Run fastqc on every FASTQ file.
2. Trim adapters with fastp.
3. Align and capture the alignment rate per sample.
4. Emit a per-sample QC summary table; flag samples below 70% alignment.

See reference/thresholds.md for the exact cutoffs.