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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 38 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 bot 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 bot found potential problems Dec 18, 2025
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docker/ngsep/Dockerfile
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FROM eclipse-temurin:8

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Medium severity - Directory Traversal vulnerability in pam High

This file introduces a vulnerable pam package with a medium severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - Allocation of Resources Without Limits or Throttling vulnerability in glibc High

This file introduces a vulnerable glibc package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Medium severity - Open Redirect vulnerability in wget Medium

This file introduces a vulnerable wget package with a medium severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Medium severity - Directory Traversal vulnerability in tar Warning

This file introduces a vulnerable tar package with a medium severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-0167 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2024-41996 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-10148 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2024-56433 vulnerability in shadow Note

This file introduces a vulnerable shadow package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Low severity - Out-of-bounds Read vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.
@adthrasher adthrasher changed the title feat: minimap2 feat: aligners & variant callers Dec 22, 2025
github-advanced-security[bot]
github-advanced-security bot found potential problems Jan 15, 2026
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docker/ngsep/Dockerfile
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FROM eclipse-temurin:8

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Low severity - CVE-2025-15224 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-15079 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-14819 vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - Open Redirect vulnerability in curl Note

This file introduces a vulnerable curl package with a low severity vulnerability.
github-advanced-security[bot]
github-advanced-security bot found potential problems Jan 20, 2026
View reviewed changes
docker/ngsep/Dockerfile
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Medium severity - Improper Verification of Cryptographic Signature vulnerability in gnupg2 Medium

This file introduces a vulnerable gnupg2 package with a medium severity vulnerability.
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 2, 2026
View reviewed changes
docker/ngsep/Dockerfile
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FROM eclipse-temurin:8

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Medium severity - CVE-2026-0861 vulnerability in glibc Warning

This file introduces a vulnerable glibc package with a medium severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Medium severity - CVE-2025-28164 vulnerability in libpng1.6 Warning

This file introduces a vulnerable libpng1.6 package with a medium severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Medium severity - CVE-2025-15467 vulnerability in openssl Warning

This file introduces a vulnerable openssl package with a medium severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2026-22795 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2026-22796 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-69418 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-69419 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-69420 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-69421 vulnerability in openssl Note

This file introduces a vulnerable openssl package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:8

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Code scanning / Snyk Container

Low severity - CVE-2025-68160 vulnerability in openssl Note

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