From d61a1408f8346492b32fd4eacf4fc6cadc3186d6 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 18 Nov 2025 02:55:19 +0000
Subject: [PATCH 1/2] chore(deps): update actions/checkout digest to 93cb6ef

---
 .github/workflows/changelog.yml                             | 2 +-
 .github/workflows/create-lint-wf.yml                        | 2 +-
 .github/workflows/create-test-lint-wf-template.yml          | 4 ++--
 .github/workflows/create-test-wf.yml                        | 2 +-
 .github/workflows/deploy-pypi.yml                           | 2 +-
 .github/workflows/fix-linting.yml                           | 2 +-
 .github/workflows/lint-code.yml                             | 2 +-
 .github/workflows/nextflow-source-test.yml                  | 4 ++--
 .github/workflows/push_dockerhub_dev.yml                    | 2 +-
 .github/workflows/push_dockerhub_release.yml                | 2 +-
 .github/workflows/pytest.yml                                | 6 +++---
 .github/workflows/sync.yml                                  | 4 ++--
 .github/workflows/test_offline_configs.yml                  | 4 ++--
 .github/workflows/update-template-snapshots.yml             | 4 ++--
 .github/workflows/update-textual-snapshots.yml              | 2 +-
 nf_core/pipeline-template/.github/workflows/fix_linting.yml | 2 +-
 nf_core/pipeline-template/.github/workflows/linting.yml     | 4 ++--
 nf_core/pipeline-template/.github/workflows/nf-test.yml     | 4 ++--
 .../.github/workflows/template-version-comment.yml          | 2 +-
 19 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index b4bf3b7a77..682a834b4c 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 98fe676348..fa7a0f6ae7 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -42,7 +42,7 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out source-code repository
 
       # Set up nf-core/tools
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index cf2cbb54c6..f70ed7014f 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -32,7 +32,7 @@ jobs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: checkout
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -56,7 +56,7 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 40b0f8e00e..91b80c3657 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -41,7 +41,7 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out source-code repository
 
       - name: Set up Python 3.14
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 0f812d2380..c1a392f45b 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out source-code repository
 
       - name: Set up Python 3.14
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index b68dcdd189..3fd67bf0a9 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 3cd598b01c..ea771554e0 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
diff --git a/.github/workflows/nextflow-source-test.yml b/.github/workflows/nextflow-source-test.yml
index df8ede5b5b..0b1614ab31 100644
--- a/.github/workflows/nextflow-source-test.yml
+++ b/.github/workflows/nextflow-source-test.yml
@@ -14,12 +14,12 @@ jobs:
 
     steps:
       - name: Check out Nextflow
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           repository: nextflow-io/nextflow
           path: nextflow
 
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out nf-core/tools
         with:
           ref: dev
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 9bc80434ea..9224eabbde 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up QEMU for multi-architecture build
         uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130 # v3
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
index 4a31a25bbd..7121eea6af 100644
--- a/.github/workflows/push_dockerhub_release.yml
+++ b/.github/workflows/push_dockerhub_release.yml
@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up QEMU for multi-architecture build
         uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130 # v3
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index fed3698f36..e9a95090fa 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -35,7 +35,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out source-code repository
 
       - name: List tests
@@ -64,7 +64,7 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
@@ -138,7 +138,7 @@ jobs:
       - runs-on=${{ github.run_id }}-coverage
       - runner=2cpu-linux-x64
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 868489b0ab..4426256663 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -62,12 +62,12 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
 
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
diff --git a/.github/workflows/test_offline_configs.yml b/.github/workflows/test_offline_configs.yml
index 225142716e..ebf9c3d6bd 100644
--- a/.github/workflows/test_offline_configs.yml
+++ b/.github/workflows/test_offline_configs.yml
@@ -53,11 +53,11 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml
index 8437bc6ecc..37fd771641 100644
--- a/.github/workflows/update-template-snapshots.yml
+++ b/.github/workflows/update-template-snapshots.yml
@@ -17,7 +17,7 @@ jobs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: checkout
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Create Matrix
         id: create_matrix
@@ -36,7 +36,7 @@ jobs:
       fail-fast: false
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
index e03825293c..015da3ef2c 100644
--- a/.github/workflows/update-textual-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
index adc5193696..eb91004e21 100644
--- a/nf_core/pipeline-template/.github/workflows/fix_linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 016961520f..1dd75aaad8 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml
index 56d862085b..e83129aa84 100644
--- a/nf_core/pipeline-template/.github/workflows/nf-test.yml
+++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml
@@ -41,7 +41,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -87,7 +87,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
diff --git a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
index 95cb23d52b..46e59e5cad 100644
--- a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
+++ b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

From 2786cf4f502f85cbbbd00cee4b67a9d6e3785573 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 18 Nov 2025 09:16:28 +0000
Subject: [PATCH 2/2] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 26d3c7faa5..9dbb239ded 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@
 - chore(deps): update mcr.microsoft.com/devcontainers/base:debian docker digest to 2e826a6 ([#3893](https://github.com/nf-core/tools/pull/3893))
 - Fix GH API rate limits. ([#3895](https://github.com/nf-core/tools/pull/3895))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.5 ([#3900](https://github.com/nf-core/tools/pull/3900))
+- Update actions/checkout digest to 93cb6ef ([#3906](https://github.com/nf-core/tools/pull/3906))
 
 ### Template