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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 86 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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github-advanced-security bot found potential problems Mar 17, 2026
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docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check failure

Code scanning / Snyk Container

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

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

Check failure

Code scanning / Snyk Container

Medium severity - Directory Traversal vulnerability in pam

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

Check warning

Code scanning / Snyk Container

Medium severity - Out-of-Bounds vulnerability in binutils

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

Check warning

Code scanning / Snyk Container

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

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

Check notice

Code scanning / Snyk Container

Medium severity - Out-of-Bounds vulnerability in binutils

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

Check notice

Code scanning / Snyk Container

Low severity - Out-of-bounds Write vulnerability in gnupg2

This file introduces a vulnerable gnupg2 package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check notice

Code scanning / Snyk Container

Low severity - Covert Timing Channel vulnerability in libgcrypt20

This file introduces a vulnerable libgcrypt20 package with a low severity vulnerability.
docker/ngsep/Dockerfile
@@ -0,0 +1,5 @@
FROM eclipse-temurin:21

Check notice

Code scanning / Snyk Container

Low severity - CVE-2024-56433 vulnerability in shadow

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