From 8972d0e01cd7c163d2e40cac05376a438c22fbd4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 22 Jun 2026 19:49:07 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black-pre-commit-mirror: 26.3.1 → 26.5.1](https://github.com/psf/black-pre-commit-mirror/compare/26.3.1...26.5.1)
- [github.com/lorenzwalthert/precommit: v0.4.3.9021 → v0.4.3.9026](https://github.com/lorenzwalthert/precommit/compare/v0.4.3.9021...v0.4.3.9026)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4e799cd..ad9fbb6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -22,12 +22,12 @@ repos:
         # https://github.com/codespell-project/codespell/issues/1498
   # Python formatting
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 26.3.1
+    rev: 26.5.1
     hooks:
       - id: black
   # R formatting
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9021
+    rev: v0.4.3.9026
     hooks:
       - id: style-files
   # general linting

From 9fced7a26c4b6286863200a5b952bfacd8ce1bfb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 22 Jun 2026 19:49:48 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .github/copilot-instructions.md | 24 ++++++++++++------------
 SECURITY.md                     |  3 +--
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index ab79ac9..d54d055 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -148,17 +148,17 @@ Example:
 
 ```json
 {
-  "Insert CRAFT prompt": {
-    "prefix": "craft",
-    "body": [
-      "/* C: Context: Repo=${workspaceFolderBasename}; bioinformatics pipelines; NIH HPC (Biowulf/Helix); containers: quay.io/ccbr */",
-      "/* R: Rules: no PHI, no secrets, containerize, pin versions, follow style */",
-      "/* F: Flow: inputs/ -> results/, conf/, tests/ */",
-      "/* T: Tests: provide a one-line TEST_CMD and expected output */",
-      "",
-      "A: $1"
-    ],
-    "description": "Insert CRAFT prompt and place cursor at Actions"
-  }
+    "Insert CRAFT prompt": {
+        "prefix": "craft",
+        "body": [
+            "/* C: Context: Repo=${workspaceFolderBasename}; bioinformatics pipelines; NIH HPC (Biowulf/Helix); containers: quay.io/ccbr */",
+            "/* R: Rules: no PHI, no secrets, containerize, pin versions, follow style */",
+            "/* F: Flow: inputs/ -> results/, conf/, tests/ */",
+            "/* T: Tests: provide a one-line TEST_CMD and expected output */",
+            "",
+            "A: $1"
+        ],
+        "description": "Insert CRAFT prompt and place cursor at Actions"
+    }
 }
 ```
diff --git a/SECURITY.md b/SECURITY.md
index 28421a0..99da43f 100644
--- a/SECURITY.md
+++ b/SECURITY.md
@@ -2,7 +2,7 @@
 
 ## Maintained Versions
 
-Actively maintained versions of contained software will vary from repository to repository, or may not be relevant at all.  
+Actively maintained versions of contained software will vary from repository to repository, or may not be relevant at all.
 The developers of this repository will update this section if any actively maintained versions of the software need to be publicly disclosed. Otherwise, contact the developers directly for any version information.
 
 ## Vulnerability Disclosure:
@@ -16,4 +16,3 @@ Follow the instructions listed in the [HHS vulnerability disclosure policy](http
 1. Click on the **Security and quality** tab of this repository.
 2. Locate the **Report a vulnerability** button. If the button is not on the **Security and quality** landing page, look under the **Advisories** section in the side bar.
 3. Click the **Report a vulnerability** button and submit the form. The developers will receive a notification of your submission.
-