Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add thesecondfox/skill --skill bio-workflows-tcr-pipelinegit clone --depth 1 https://github.com/thesecondfox/skillWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-workflows-tcr-pipeline)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-workflows-tcr-pipeline"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-workflows-tcr-pipeline/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-workflows-tcr-pipeline"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-workflows-tcr-pipeline.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00040 | $0.00558 |
| Opus 5 | $0.00020 | $0.00279 |
| Sonnet 5 | $0.00008 | $0.00112 |
| Haiku 4.5 | $0.00004 | $0.00056 |
Grade A, and why
bio-workflows-tcr-pipeline scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
Version Compatibility
Reference examples tested with: MiXCR 4.6+, VDJtools 1.2.1+
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
TCR/BCR Analysis Pipeline
"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.
Pipeline Overview
FASTQ → MiXCR align → Assemble → Export → VDJtools diversity → Visualization
Step 1: MiXCR Processing
# 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
Step 2: VDJtools Analysis
# 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/
Step 3: Visualization
# Spectratype plot
vdjtools PlotFancySpectratype vdjtools/clones.txt spectra/
# V usage
vdjtools PlotFancyVJUsage vdjtools/clones.txt usage/
QC Checkpoints
- After alignment: Check V/J assignment rate (>70% typical)
- After assembly: Verify clonotype count and coverage
- After diversity: Compare metrics to expected range
Related Skills
- tcr-bcr-analysis/mixcr-analysis - Detailed MiXCR usage
- tcr-bcr-analysis/vdjtools-analysis - Diversity metrics
- tcr-bcr-analysis/repertoire-visualization - Plots
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 5d ago First seen · 77 lines · 40 tokens per session scan A cc125100b2a5
bio-workflows-tcr-pipeline is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 40 tokens to every session and 558 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
exploratory-data-analysis
Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…
matlab
Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
phylogenetics
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
research-engineer
An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.
mapping-to-snomed
Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…