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feat: aligners & variant callers#282

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feat/minimap2
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feat: aligners & variant callers#282
adthrasher wants to merge 116 commits intomainfrom
feat/minimap2

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@adthrasher adthrasher commented Dec 3, 2025 •
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Adds new WDL task implementations:

  • bwa-mem2
  • minimap2
  • hisat2
  • vg giraffe
  • DeepVariant / DeepSomatic
  • Strelka
  • Manta
  • Clair3
  • NGSEP

Before submitting this PR, please make sure:

  • You have added a few sentences describing the PR here.
  • The code passes all CI tests without any errors or warnings.
  • You have added tests (when appropriate).
  • You have added an entry in any relevant CHANGELOGs (when appropriate).
  • If you have made any changes to the scripts/ or docker/ directories, please ensure any image versions have been incremented accordingly!
  • You have updated the README or other documentation to account for these changes (when appropriate).

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github-advanced-security AI commented Dec 3, 2025

This pull request sets up GitHub code scanning for this repository. Once the scans have completed and the checks have passed, the analysis results for this pull request branch will appear on this overview. Once you merge this pull request, the 'Security' tab will show more code scanning analysis results (for example, for the default branch). Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results. For more information about GitHub code scanning, check out the documentation.

@adthrasher adthrasher marked this pull request as draft December 9, 2025 16:12
@adthrasher adthrasher self-assigned this Dec 9, 2025
github-advanced-security[bot]
github-advanced-security AI found potential problems Dec 18, 2025
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Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
Comment thread docker/ngsep/Dockerfile Fixed
github-advanced-security[bot]
github-advanced-security AI found potential problems Mar 27, 2026
View reviewed changes
Comment thread docker/ngsep/Dockerfile Fixed
github-advanced-security[bot]
github-advanced-security AI found potential problems Apr 17, 2026
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Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2025-69648 vulnerability in binutils Warning

This file introduces a vulnerable binutils package with a medium severity vulnerability.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2025-69647 vulnerability in binutils Warning

This file introduces a vulnerable binutils package with a medium severity vulnerability.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2025-69644 vulnerability in binutils Warning

This file introduces a vulnerable binutils package with a medium severity vulnerability.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2025-69652 vulnerability in binutils Warning

This file introduces a vulnerable binutils package with a medium severity vulnerability.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2025-69651 vulnerability in binutils Medium

This file introduces a vulnerable binutils package with a medium severity vulnerability.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2025-69645 vulnerability in binutils Warning

This file introduces a vulnerable binutils package with a medium severity vulnerability.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2025-69646 vulnerability in binutils Warning

This file introduces a vulnerable binutils package with a medium severity vulnerability.
github-advanced-security[bot]
github-advanced-security AI found potential problems Apr 24, 2026
View reviewed changes
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

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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.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

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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.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

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Code scanning / Snyk Container

Medium severity - Time-of-check Time-of-use (TOCTOU) vulnerability in libcap2 High

This file introduces a vulnerable libcap2 package with a medium severity vulnerability.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

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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.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

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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.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

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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.
Comment thread docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check warning

Code scanning / Snyk Container

Medium severity - CVE-2026-2219 vulnerability in dpkg Warning

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