diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index b4bf3b7a77..917a8127df 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -1,7 +1,7 @@
 name: Update CHANGELOG.md
 on:
   issue_comment:
-    types: [created]
+    types: [created] # Add "@nf-core-bot changelog" as a PR comment to trigger this workflow.
   pull_request_target:
     types: [opened]
     branches:
@@ -10,15 +10,17 @@ on:
 jobs:
   update_changelog:
     runs-on: ubuntu-latest
-    # Run if comment is on a PR with the main repo, and if it contains the magic keywords.
-    # Or run on PR creation, unless asked otherwise in the title.
-    if: |
-      github.repository_owner == 'nf-core' && (
-        github.event_name == 'pull_request_target' ||
-        github.event.issue.pull_request && startsWith(github.event.comment.body, '@nf-core-bot changelog')
-      )
 
     steps:
+      - name: branch-deploy
+        id: branch-deploy
+        if: github.event_name == 'issue_comment'
+        uses: github/branch-deploy@c9fcc362bdcea69eecac6578dde245cd5e3a55bf # v10.4.3
+        with:
+          trigger: "@nf-core-bot changelog"
+          reaction: "eyes"
+          stable_branch: "dev"
+
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index b68dcdd189..30fa7ba33f 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -1,29 +1,28 @@
 name: Fix linting from a comment
 on:
   issue_comment:
-    types: [created]
+    types: [created] # Add "@nf-core-bot fix linting" as a PR comment to trigger this workflow.
 
 jobs:
   fix-linting:
-    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
-    if: >
-      contains(github.event.comment.html_url, '/pull/') &&
-      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/tools'
     runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+
     steps:
+      - name: branch-deploy
+        id: branch-deploy
+        uses: github/branch-deploy@c9fcc362bdcea69eecac6578dde245cd5e3a55bf # v10.4.3
+        with:
+          trigger: "@nf-core-bot fix linting"
+          reaction: "eyes"
+          stable_branch: "dev"
+
       # Use the @nf-core-bot token to check out so we can push later
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
-      # indication that the linting is being fixed
-      - name: React on comment
-        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: eyes
-
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml
index 8437bc6ecc..eeb44720c6 100644
--- a/.github/workflows/update-template-snapshots.yml
+++ b/.github/workflows/update-template-snapshots.yml
@@ -1,21 +1,26 @@
 name: Update Template snapshots from a comment
 on:
   issue_comment:
-    types: [created]
+    types: [created] # Add "@nf-core-bot update template snapshots" as a PR comment to trigger this workflow.
 
 jobs:
   prepare-matrix:
     name: Retrieve all template features
-    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
-    if: >
-      contains(github.event.comment.html_url, '/pull/') &&
-      contains(github.event.comment.body, '@nf-core-bot') &&
-      contains(github.event.comment.body, 'update template snapshots') &&
-      github.repository == 'nf-core/tools'
     runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
     outputs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
+
     steps:
+      - name: branch-deploy
+        id: branch-deploy
+        uses: github/branch-deploy@c9fcc362bdcea69eecac6578dde245cd5e3a55bf # v10.4.3
+        with:
+          trigger: "@nf-core-bot update template snapshots"
+          reaction: "eyes"
+          stable_branch: "dev"
+
       - name: checkout
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
@@ -28,6 +33,8 @@ jobs:
   update-snapshots:
     needs: [prepare-matrix]
     runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
     strategy:
       matrix:
         TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
@@ -40,13 +47,6 @@ jobs:
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
-      # indication that the command is running
-      - name: React on comment
-        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: eyes
-
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
index e03825293c..e3003aeee4 100644
--- a/.github/workflows/update-textual-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -1,18 +1,21 @@
 name: Update Textual snapshots from a comment
 on:
   issue_comment:
-    types: [created]
+    types: [created] # Add "@nf-core-bot update textual snapshots" as a PR comment to trigger this workflow.
 
 jobs:
   update-snapshots:
-    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
-    if: >
-      contains(github.event.comment.html_url, '/pull/') &&
-      contains(github.event.comment.body, '@nf-core-bot') &&
-      contains(github.event.comment.body, 'update textual snapshots') &&
-      github.repository == 'nf-core/tools'
     runs-on: ubuntu-latest
+
     steps:
+      - name: branch-deploy
+        id: branch-deploy
+        uses: github/branch-deploy@c9fcc362bdcea69eecac6578dde245cd5e3a55bf # v10.4.3
+        with:
+          trigger: "@nf-core-bot update textual snapshots"
+          reaction: "eyes"
+          stable_branch: "dev"
+
       # Use the @nf-core-bot token to check out so we can push later
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with: