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chore: add AGENTS file for AI tools

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feat: aligners & variant callers #282

chore: add AGENTS file for AI tools
5a596c1
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GitHub Advanced Security / Snyk Container completed May 12, 2026 in 2s

6 configurations not found

Warning: Code scanning may not have found all the alerts introduced by this pull request, because 6 configurations present on refs/heads/main were not found:

Actions workflow (build-and-test.yaml)

  • ❓  Snyk/Container/docker-image|ghcr.io/stjudecloud/bwa
  • ❓  Snyk/Container/docker-image|ghcr.io/stjudecloud/minfi
  • ❓  Snyk/Container/docker-image|ghcr.io/stjudecloud/pandas
  • ❓  Snyk/Container/docker-image|ghcr.io/stjudecloud/python-plotting
  • ❓  Snyk/Container/docker-image|ghcr.io/stjudecloud/umap
  • ❓  Snyk/Container/docker-image|ghcr.io/stjudecloud/util

New alerts in code changed by this pull request

Security Alerts:

  • 9 medium

Other Alerts:

  • 25 warnings
  • 2 notes

See annotations below for details.

View all branch alerts.

Annotations

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Allocation of Resources Without Limits or Throttling vulnerability in binutils Medium

This file introduces a vulnerable binutils package with a low severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35371 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35364 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35351 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35345 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35360 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35363 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35344 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35352 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35359 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35377 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Time-of-check Time-of-use (TOCTOU) vulnerability in sed Warning

This file introduces a vulnerable sed package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Directory Traversal vulnerability in tar Warning

This file introduces a vulnerable tar package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Unrestricted Upload of File with Dangerous Type vulnerability in tar Medium

This file introduces a vulnerable tar package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Time-of-check Time-of-use (TOCTOU) vulnerability in util-linux Warning

This file introduces a vulnerable util-linux package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Authentication Bypass vulnerability in util-linux Medium

This file introduces a vulnerable util-linux package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Open Redirect vulnerability in wget Medium

This file introduces a vulnerable wget package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Heap-based Buffer Overflow vulnerability in openjdk-jre Medium

This file introduces a vulnerable openjdk-jre package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Algorithmic Complexity vulnerability in expat Medium

This file introduces a vulnerable expat package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-4437 vulnerability in glibc Warning

This file introduces a vulnerable glibc package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-4438 vulnerability in glibc Warning

This file introduces a vulnerable glibc package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-4046 vulnerability in glibc Warning

This file introduces a vulnerable glibc package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - Algorithmic Complexity vulnerability in gnutls28 Medium

This file introduces a vulnerable gnutls28 package with a medium severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Low severity - Stack-based Buffer Overflow vulnerability in gnutls28 Medium

This file introduces a vulnerable gnutls28 package with a low severity vulnerability.

Check warning on line 1 in docker/ngsep/Dockerfile

See this annotation in the file changed.

Code scanning / Snyk Container

Medium severity - CVE-2026-35350 vulnerability in rust-coreutils Warning

This file introduces a vulnerable rust-coreutils package with a medium severity vulnerability.