bio-reporting-automated-qc-reports — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited bio-reporting-automated-qc-reports (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
Reference examples tested with: Cell Ranger 8.0+, FastQC 0.12+, GATK 4.5+, HISAT2 2.2.1+, MultiQC 1.21+, STAR 2.7.11+, Subread 2.0+, bcftools 1.19+, fastp 0.23+, kallisto 0.50+
Before using code patterns, verify installed versions match. If versions differ:
pip show <package> then help(module.function) to check signatures<tool> --version then <tool> --help to confirm flagsIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"Aggregate QC results into one report" → Combine outputs from FastQC, samtools, Picard, and other tools into a single interactive HTML report.
multiqc . (scans current directory for recognized tool outputs)# Aggregate all QC outputs in directory
multiqc results/ -o qc_report/
# Specify output name
multiqc results/ -n my_project_qc
# Include specific tools only
multiqc results/ --module fastqc --module starMultiQC recognizes outputs from 100+ bioinformatics tools:
| Category | Tools |
|---|---|
| Read QC | FastQC, fastp, Cutadapt |
| Alignment | STAR, HISAT2, BWA, Bowtie2 |
| Quantification | featureCounts, Salmon, kallisto |
| Variant Calling | bcftools, GATK |
| Single-cell | CellRanger, STARsolo |
Create multiqc_config.yaml:
title: "RNA-seq QC Report"
subtitle: "Project XYZ"
intro_text: "QC metrics for all samples"
# Custom sample name cleaning
extra_fn_clean_exts:
- '.sorted'
- '.dedup'
# Report sections to include
module_order:
- fastqc
- star
- featurecounts
# Highlight samples
table_cond_formatting_rules:
pct_mapped:
fail: [{lt: 50}]
warn: [{lt: 70}]# Add custom data file
# File format: sample\tmetric1\tmetric2
multiqc results/ --data-format tsv --custom-data-file custom_metrics.tsvfrom multiqc import run as multiqc_run
# Run programmatically
multiqc_run(analysis_dir='results/', outdir='qc_report/')~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.