From a8988f4be3d462fd18f4f3076d800f1fffddee43 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 19:51:15 +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: 26.3.0 → 26.3.1](https://github.com/psf/black-pre-commit-mirror/compare/26.3.0...26.3.1)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a6e75cc..8517aca 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -27,7 +27,7 @@ repos:
         # https://github.com/codespell-project/codespell/issues/1498
   # Python formatting
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 26.3.0
+    rev: 26.3.1
     hooks:
       - id: black
   # R formatting

From cfbd7c32c4ab72d852964831f372a49e3e933f53 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 19:54:28 +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 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 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"
+    }
 }
 ```