bio-workflows-tcr-pipeline — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited bio-workflows-tcr-pipeline (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: MiXCR 4.6+, VDJtools 1.2.1+
Before using code patterns, verify installed versions match. If versions differ:
<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.
"Analyze my TCR/BCR repertoire sequencing data end-to-end" → Orchestrate MiXCR clonotype extraction, VDJtools diversity/repertoire analysis, Immcantation SHM and lineage analysis, and visualization of V/J gene usage and clonal dynamics.
FASTQ → MiXCR align → Assemble → Export → VDJtools diversity → Visualization# Align reads to V(D)J segments
mixcr align -s hsa -p rna-seq \
R1.fastq.gz R2.fastq.gz \
aligned.vdjca
# Assemble clonotypes
mixcr assemble aligned.vdjca clones.clns
# Export
mixcr exportClones clones.clns clones.txt# Convert to VDJtools format
vdjtools Convert -S mixcr clones.txt vdjtools/
# Diversity metrics
vdjtools CalcDiversityStats vdjtools/clones.txt diversity/
# Sample overlap
vdjtools CalcPairwiseDistances vdjtools/*.txt overlap/# Spectratype plot
vdjtools PlotFancySpectratype vdjtools/clones.txt spectra/
# V usage
vdjtools PlotFancyVJUsage vdjtools/clones.txt usage/~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.