Sc Fastq Qc

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “/sc-fastq-qc”

Requirements

• Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

1. 1Discover FASTQ files and choose one sample (--sample disambiguates a directory).
2. 2Summarize the first --max-reads records per file in Python.
3. 3Run FastQC when present, then MultiQC when both tools are present.
4. 4Render four figures from the Python summaries; external HTML is separate.
5. 5Write three tables, report.md and result.json.

What it can do on your machine

Read from SKILL.md and the folder at commit 90a3bec. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Sc Fastq Qc loads about 1k tokens when it runs, and up to ~3.5k if it reads all its reference files. Until then it costs about 49 tokens; SKILL.md has 342 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~49

When it runs · the whole SKILL.md, loaded when a task matches

~1k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~3.5k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 342 words, ~1,028 tokens.

name

sc-fastq-qc

description

Load when checking raw single-cell FASTQ read quality (Phred / GC / adapter / length) before counting. Skip when reads are already counted (use sc-qc); bulk FASTQ (use bulkrna-read-qc).

trigger

scRNA FASTQ QC, FastQC single-cell, MultiQC single-cell, raw read quality, read-level QC

tags

singlecell, scrna, fastq, qc, read-quality

from skills._sdk.notebook import run_cli

run_cli("sc-fastq-qc", "--input", "data/sample_R1.fastq.gz",
        "--read2", "data/sample_R2.fastq.gz",
        inputs=["data/sample_R1.fastq.gz", "data/sample_R2.fastq.gz"])

# Demo (synthetic summary tables, no FASTQ or external tools)
python skills/singlecell/scrna/sc-fastq-qc/sc_fastq_qc.py --demo --output /tmp/sc_fastq_qc_demo

# Single-file with paired-end
python skills/singlecell/scrna/sc-fastq-qc/sc_fastq_qc.py \
  --input sample_R1.fastq.gz --read2 sample_R2.fastq.gz --output results/

# Choose a sample and increase Python sampling depth
python skills/singlecell/scrna/sc-fastq-qc/sc_fastq_qc.py \
  --input fastq_dir/ --sample sample_A --output results/ --max-reads 100000 --threads 8

© TianGzlab, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 7 other files (references) in skills/singlecell/scrna/sc-fastq-qc of TianGzlab/OmicsClaw.

• SKILL.md
• references/methodology.md
• references/output_contract.md
• references/parameters.md
• references/r_visualization.md
• sc_fastq_qc.py
• tests/test_fastqc_paths.py
• tests/test_sc_fastq_qc.py

Open the folder on GitHubat commit 90a3bec