The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill downloads the ENCODE blacklist, which is a standard reference dataset for genomic analysis, from the Boyle Lab's GitHub repository. This is a common and safe practice in bioinformatics workflows to filter out artifact-prone regions.
Evidence: wget https://github.com/Boyle-Lab/Blacklist/raw/master/lists/hg38-blacklist.v2.bed.gz in SKILL.md and usage-guide.md.
[COMMAND_EXECUTION]: The skill executes standard bioinformatics command-line tools including macs2, macs3, samtools, idr, and bedtools to perform genomic data processing. These operations are aligned with the skill's primary purpose.
Evidence: Invocations of macs2 callpeak, samtools view, idr --samples, and bedtools intersect within examples/call_atac_peaks.sh.
[INDIRECT_PROMPT_INJECTION]: The skill ingests external genomic data files (BAM and BED formats), which represents a surface for processing untrusted data.
Ingestion points: Input variables in examples/call_atac_peaks.sh such as REP1, REP2, and BLACKLIST.
Boundary markers: None present, as these are binary or structured data formats not typically containing natural language instructions.
Capability inventory: File system writes (mkdir, sort >) and execution of various bioinformatics CLI tools.
Sanitization: The script uses set -euo pipefail for shell safety but does not perform content validation on the genomic files themselves, which is standard for this domain.

bio-atac-seq-atac-peak-calling