From 0f32c497369c57865351067d55c6d57672d6006c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 10:39:32 +0200
Subject: [PATCH 01/21] first try for netlify deploy action

---
 .github/workflows/netlify-deploy-preview.yml | 82 ++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 .github/workflows/netlify-deploy-preview.yml

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
new file mode 100644
index 0000000000..00567048f6
--- /dev/null
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -0,0 +1,82 @@
+name: trigger Netlify deploy preview
+
+on:
+  pull_request:
+    paths: ['sites/docs/**', 'sites/main-site/**']
+
+jobs:
+  pre-build:
+    name: 'prepare build setup'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./website
+    steps:
+      - name: Checkout website repo
+        uses: actions/checkout@v4
+        with:
+          path: ./website
+
+      - name: Set up Node.js 20
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: 'npm'
+
+      - name: Install npm deps
+        run: npm ci
+
+      - name: get changed sub-site
+        id: get_changed_subsite
+        run: |
+          CHANGED_DIRECTORY=$(git diff --name-only HEAD~1 HEAD | grep 'sites/' | cut -d/ -f2 | uniq) >> $GITHUB_ENV
+
+  deploy-main-site:
+    name: 'Deploy preview for main-site'
+    runs-on: ubuntu-latest
+    needs: pre-build
+    if: github.repository == 'nf-core/website' && env.CHANGED_DIRECTORY == 'docs'
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Build website
+        run: npm run build --workspace sites/main-site
+
+      - name: Deploy to Netlify
+        uses: nwtgck/actions-netlify@v3.0.0
+        with:
+          publish-dir: './sites/main-site/dist'
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message: 'nf-core/main-site PR #${{ github.event.pull_request.number }}: ${{ github.event.pull_request.title }}'
+          alias: nf-core-main-site-pr-${{ github.event.pull_request.number }}
+          enable-commit-comment: false
+          enable-commit-status: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_MAIN_SITE_ID }}
+        timeout-minutes: 1
+
+  deploy-docs:
+    name: 'Deploy preview for docs'
+    runs-on: ubuntu-latest
+    needs: pre-build
+    if: github.repository == 'nf-core/website'
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Build website
+        run: npm run build --workspace sites/docs
+
+      - name: Deploy to Netlify
+        uses: nwtgck/actions-netlify@v3.0.0
+        with:
+          publish-dir: './sites/docs/dist'
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message: 'nf-core/docs PR #${{ github.event.pull_request.number }}: ${{ github.event.pull_request.title }}'
+          alias: nf-core-docs-pr-${{ github.event.pull_request.number }}
+          enable-commit-comment: false
+          enable-commit-status: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_DOCS_ID }}
+        timeout-minutes: 1

From 8487560c7e690721e50b2b11980fd53d647215bd Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 10:41:37 +0200
Subject: [PATCH 02/21] fix new post badge

---
 sites/main-site/src/pages/blog/index.astro | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sites/main-site/src/pages/blog/index.astro b/sites/main-site/src/pages/blog/index.astro
index 0473f7b64c..317fc0ad99 100644
--- a/sites/main-site/src/pages/blog/index.astro
+++ b/sites/main-site/src/pages/blog/index.astro
@@ -82,7 +82,7 @@ const sections: SidebarEntry[] = years.map((year) => {
                                         <a
                                             href={'/blog/' + post.slug}
                                             class:list={[
-                                                'post-badge text-decoration-none badge text-bg-primary fs-6 mb-0  rounded-top-0 w-25 m-auto position-absolute top-0 start-0 end-0',
+                                                'post-badge text-decoration-none badge text-bg-primary fs-6 mb-0 rounded-top-0 m-auto position-absolute top-0 start-0 end-0',
                                                 new Date(Date.now()) > new Date(post.data.pubDate) &&
                                                 new Date(post.data.pubDate) >
                                                     new Date(Date.now() - 2 * 24 * 60 * 60 * 1000)
@@ -168,5 +168,6 @@ const sections: SidebarEntry[] = years.map((year) => {
     }
     .post-badge {
         z-index: 10;
+        width: fit-content;
     }
 </style>

From 34a7e9a7cb1084c370d0560f0129577d8825f71f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 10:43:55 +0200
Subject: [PATCH 03/21] try different syntax

---
 .github/workflows/netlify-deploy-preview.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 00567048f6..8808318609 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -30,12 +30,14 @@ jobs:
         id: get_changed_subsite
         run: |
           CHANGED_DIRECTORY=$(git diff --name-only HEAD~1 HEAD | grep 'sites/' | cut -d/ -f2 | uniq) >> $GITHUB_ENV
+    outputs:
+      changed_directory: ${{ env.CHANGED_DIRECTORY }}
 
   deploy-main-site:
     name: 'Deploy preview for main-site'
     runs-on: ubuntu-latest
     needs: pre-build
-    if: github.repository == 'nf-core/website' && env.CHANGED_DIRECTORY == 'docs'
+    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory == 'main-site'
     permissions:
       pull-requests: write
     steps:
@@ -60,7 +62,7 @@ jobs:
     name: 'Deploy preview for docs'
     runs-on: ubuntu-latest
     needs: pre-build
-    if: github.repository == 'nf-core/website'
+    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory == 'docs'
     permissions:
       pull-requests: write
     steps:

From ee5fff64cc58633c63cb101c3db0de389e3f0431 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 10:46:23 +0200
Subject: [PATCH 04/21] debug action

---
 .github/workflows/netlify-deploy-preview.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 8808318609..0c0b6de5fc 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -26,6 +26,12 @@ jobs:
       - name: Install npm deps
         run: npm ci
 
+      - name: debug
+        run: |
+          ls -l .
+          ls -l ..
+          pwd
+
       - name: get changed sub-site
         id: get_changed_subsite
         run: |
@@ -36,6 +42,9 @@ jobs:
   deploy-main-site:
     name: 'Deploy preview for main-site'
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./website
     needs: pre-build
     if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory == 'main-site'
     permissions:
@@ -61,6 +70,9 @@ jobs:
   deploy-docs:
     name: 'Deploy preview for docs'
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./website
     needs: pre-build
     if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory == 'docs'
     permissions:

From 4900d72c6639afa3cd2520148a33f7769042a044 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 10:48:09 +0200
Subject: [PATCH 05/21] more debugging

---
 .github/workflows/netlify-deploy-preview.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 0c0b6de5fc..f4ee253ccc 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -16,7 +16,11 @@ jobs:
         uses: actions/checkout@v4
         with:
           path: ./website
-
+      - name: debug
+        run: |
+          ls -l .
+          ls -l ..
+          pwd
       - name: Set up Node.js 20
         uses: actions/setup-node@v4
         with:

From e0d02ddcd53e87a7763062571dd7431a9b0f183f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 10:50:39 +0200
Subject: [PATCH 06/21] specify cache-path

---
 .github/workflows/netlify-deploy-preview.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index f4ee253ccc..aff9d58fcf 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -26,6 +26,7 @@ jobs:
         with:
           node-version: 20
           cache: 'npm'
+          cache-dependency-path: ./website/package-lock.json
 
       - name: Install npm deps
         run: npm ci

From 21d5b31105035ef0dcfd5e6b06796d0a82af5cb5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:00:01 +0200
Subject: [PATCH 07/21] try new git diff strategy

---
 .github/workflows/netlify-deploy-preview.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index aff9d58fcf..0b785c3c53 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -40,7 +40,7 @@ jobs:
       - name: get changed sub-site
         id: get_changed_subsite
         run: |
-          CHANGED_DIRECTORY=$(git diff --name-only HEAD~1 HEAD | grep 'sites/' | cut -d/ -f2 | uniq) >> $GITHUB_ENV
+          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2) >> $GITHUB_ENV
     outputs:
       changed_directory: ${{ env.CHANGED_DIRECTORY }}
 

From dd453d0fc898fc7a74fde0a7042b73454844e1ea Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:03:36 +0200
Subject: [PATCH 08/21] try different variable

---
 .github/workflows/netlify-deploy-preview.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 0b785c3c53..f6634fe89a 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -40,7 +40,7 @@ jobs:
       - name: get changed sub-site
         id: get_changed_subsite
         run: |
-          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2) >> $GITHUB_ENV
+          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.event.before }} HEAD | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2) >> $GITHUB_ENV
     outputs:
       changed_directory: ${{ env.CHANGED_DIRECTORY }}
 

From 8393dbd15746926dd659f6c612e51622d7380d3c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:06:07 +0200
Subject: [PATCH 09/21] yet another variable

---
 .github/workflows/netlify-deploy-preview.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index f6634fe89a..72d00d3b69 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -40,7 +40,7 @@ jobs:
       - name: get changed sub-site
         id: get_changed_subsite
         run: |
-          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.event.before }} HEAD | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2) >> $GITHUB_ENV
+          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}...${{ github.head_ref }} | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2)
     outputs:
       changed_directory: ${{ env.CHANGED_DIRECTORY }}
 

From 88361b7fb0d89fd14ce86f51fe1b47fdaaf912d0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:15:06 +0200
Subject: [PATCH 10/21] try another comparison

---
 .github/workflows/netlify-deploy-preview.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 72d00d3b69..ebeef0bbe9 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -40,7 +40,7 @@ jobs:
       - name: get changed sub-site
         id: get_changed_subsite
         run: |
-          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}...${{ github.head_ref }} | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2)
+          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}...HEAD | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2)
     outputs:
       changed_directory: ${{ env.CHANGED_DIRECTORY }}
 

From e392b7573015a44ba3fecb42d9c6f99dc375b774 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:17:43 +0200
Subject: [PATCH 11/21] more git debugging

---
 .github/workflows/netlify-deploy-preview.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index ebeef0bbe9..7e628fdf8b 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -36,6 +36,7 @@ jobs:
           ls -l .
           ls -l ..
           pwd
+          git status
 
       - name: get changed sub-site
         id: get_changed_subsite

From a066dbe6533946deac480364d10c66f52b63a24f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:20:42 +0200
Subject: [PATCH 12/21] yet another diff try

---
 .github/workflows/netlify-deploy-preview.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 7e628fdf8b..bdccd8dd77 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -41,7 +41,7 @@ jobs:
       - name: get changed sub-site
         id: get_changed_subsite
         run: |
-          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}...HEAD | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2)
+          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}.HEAD | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2)
     outputs:
       changed_directory: ${{ env.CHANGED_DIRECTORY }}
 

From a165d00e13a4953e63c29553371407cf5185d942 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:23:30 +0200
Subject: [PATCH 13/21] another try

---
 .github/workflows/netlify-deploy-preview.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index bdccd8dd77..d9aff5b36b 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -41,7 +41,7 @@ jobs:
       - name: get changed sub-site
         id: get_changed_subsite
         run: |
-          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}.HEAD | grep -E 'sites/(main-site|docs)' | head -n1 | cut -d'/' -f2)
+          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}...${{github.head_ref}} | grep -E 'sites/(main-site|docs)' | head -n 1 | cut -d'/' -f2)
     outputs:
       changed_directory: ${{ env.CHANGED_DIRECTORY }}
 

From 0007fb08970054ea59d31a112ee73f86fc45ce7d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:29:04 +0200
Subject: [PATCH 14/21] switch diff strategy

---
 .github/workflows/netlify-deploy-preview.yml | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index d9aff5b36b..ce56be63fe 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -38,12 +38,17 @@ jobs:
           pwd
           git status
 
-      - name: get changed sub-site
-        id: get_changed_subsite
-        run: |
-          CHANGED_DIRECTORY=$(git diff --name-only ${{ github.base_ref }}...${{github.head_ref}} | grep -E 'sites/(main-site|docs)' | head -n 1 | cut -d'/' -f2)
+      - name: Check changed files
+        id: changed-files-yaml
+        uses: tj-actions/changed-files@v44
+        with:
+          files_yaml: |
+            docs:
+              - sites/docs/**
+            main-site:
+              - sites/main-site/**
     outputs:
-      changed_directory: ${{ env.CHANGED_DIRECTORY }}
+      changed_directory: ${{ env.changed_files_yaml }}
 
   deploy-main-site:
     name: 'Deploy preview for main-site'
@@ -52,7 +57,7 @@ jobs:
       run:
         working-directory: ./website
     needs: pre-build
-    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory == 'main-site'
+    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory.main-site_any_changed == 'true'
     permissions:
       pull-requests: write
     steps:
@@ -80,7 +85,7 @@ jobs:
       run:
         working-directory: ./website
     needs: pre-build
-    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory == 'docs'
+    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory.docs_any_changed == 'true'
     permissions:
       pull-requests: write
     steps:

From 5dc2f80db913008e1355740ff98dba74855807d5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:45:09 +0200
Subject: [PATCH 15/21] fix output

---
 .github/workflows/netlify-deploy-preview.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index ce56be63fe..5d959e49cf 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -48,8 +48,8 @@ jobs:
             main-site:
               - sites/main-site/**
     outputs:
-      changed_directory: ${{ env.changed_files_yaml }}
-
+      main-site_any_changed: ${{ steps.changed-files-yaml.outputs.main-site_any_changed }}
+      docs_any_changed: ${{ steps.changed-files-yaml.outputs.docs_any_changed }}
   deploy-main-site:
     name: 'Deploy preview for main-site'
     runs-on: ubuntu-latest
@@ -57,7 +57,7 @@ jobs:
       run:
         working-directory: ./website
     needs: pre-build
-    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory.main-site_any_changed == 'true'
+    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.main-site_any_changed == 'true'
     permissions:
       pull-requests: write
     steps:
@@ -85,7 +85,7 @@ jobs:
       run:
         working-directory: ./website
     needs: pre-build
-    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.changed_directory.docs_any_changed == 'true'
+    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.docs_any_changed == 'true'
     permissions:
       pull-requests: write
     steps:

From 3c36f664ff4c7da07c94598eb16a9ae7afc573fa Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 11:51:50 +0200
Subject: [PATCH 16/21] try to fix the directory path

---
 .github/workflows/netlify-deploy-preview.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 5d959e49cf..dc854e1efb 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -53,9 +53,6 @@ jobs:
   deploy-main-site:
     name: 'Deploy preview for main-site'
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: ./website
     needs: pre-build
     if: github.repository == 'nf-core/website' && needs.pre-build.outputs.main-site_any_changed == 'true'
     permissions:
@@ -81,9 +78,6 @@ jobs:
   deploy-docs:
     name: 'Deploy preview for docs'
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: ./website
     needs: pre-build
     if: github.repository == 'nf-core/website' && needs.pre-build.outputs.docs_any_changed == 'true'
     permissions:

From a670940525bbf08486809a69afe3820fef6b6916 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 12:10:26 +0200
Subject: [PATCH 17/21] add debug step

---
 .github/workflows/netlify-deploy-preview.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index dc854e1efb..f27dd404d9 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -53,11 +53,20 @@ jobs:
   deploy-main-site:
     name: 'Deploy preview for main-site'
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: website
     needs: pre-build
     if: github.repository == 'nf-core/website' && needs.pre-build.outputs.main-site_any_changed == 'true'
     permissions:
       pull-requests: write
     steps:
+      - name: debug
+        run: |
+          ls -l .
+          ls -l ..
+          pwd
+
       - name: Build website
         run: npm run build --workspace sites/main-site
 
@@ -78,6 +87,9 @@ jobs:
   deploy-docs:
     name: 'Deploy preview for docs'
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: website
     needs: pre-build
     if: github.repository == 'nf-core/website' && needs.pre-build.outputs.docs_any_changed == 'true'
     permissions:

From 08df55d2dbbf13acce860a4af173e54a1dc1131b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 12:20:37 +0200
Subject: [PATCH 18/21] restructure jobs

---
 .github/workflows/netlify-deploy-preview.yml | 68 +++++++++-----------
 1 file changed, 31 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index f27dd404d9..da5ae89f5e 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -5,38 +5,12 @@ on:
     paths: ['sites/docs/**', 'sites/main-site/**']
 
 jobs:
-  pre-build:
-    name: 'prepare build setup'
+  change-detection:
+    name: 'detect changed sub-sites'
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: ./website
     steps:
       - name: Checkout website repo
         uses: actions/checkout@v4
-        with:
-          path: ./website
-      - name: debug
-        run: |
-          ls -l .
-          ls -l ..
-          pwd
-      - name: Set up Node.js 20
-        uses: actions/setup-node@v4
-        with:
-          node-version: 20
-          cache: 'npm'
-          cache-dependency-path: ./website/package-lock.json
-
-      - name: Install npm deps
-        run: npm ci
-
-      - name: debug
-        run: |
-          ls -l .
-          ls -l ..
-          pwd
-          git status
 
       - name: Check changed files
         id: changed-files-yaml
@@ -50,22 +24,30 @@ jobs:
     outputs:
       main-site_any_changed: ${{ steps.changed-files-yaml.outputs.main-site_any_changed }}
       docs_any_changed: ${{ steps.changed-files-yaml.outputs.docs_any_changed }}
+
   deploy-main-site:
     name: 'Deploy preview for main-site'
     runs-on: ubuntu-latest
     defaults:
       run:
         working-directory: website
-    needs: pre-build
-    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.main-site_any_changed == 'true'
+    needs: change-detection
+    if: github.repository == 'nf-core/website' && needs.change-detection.outputs.main-site_any_changed == 'true'
     permissions:
       pull-requests: write
     steps:
-      - name: debug
-        run: |
-          ls -l .
-          ls -l ..
-          pwd
+      - name: Checkout website repo
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js 20
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: 'npm'
+          cache-dependency-path: ./website/package-lock.json
+
+      - name: Install npm deps
+        run: npm ci
 
       - name: Build website
         run: npm run build --workspace sites/main-site
@@ -90,11 +72,23 @@ jobs:
     defaults:
       run:
         working-directory: website
-    needs: pre-build
-    if: github.repository == 'nf-core/website' && needs.pre-build.outputs.docs_any_changed == 'true'
+    needs: change-detection
+    if: github.repository == 'nf-core/website' && needs.change-detection.outputs.docs_any_changed == 'true'
     permissions:
       pull-requests: write
     steps:
+      - name: Checkout website repo
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js 20
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: 'npm'
+          cache-dependency-path: ./website/package-lock.json
+
+      - name: Install npm deps
+        run: npm ci
       - name: Build website
         run: npm run build --workspace sites/docs
 

From d8c332f6ef17b17f5e8e21730c141ffb7cafba43 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 12:45:50 +0200
Subject: [PATCH 19/21] fix cache path

---
 .github/workflows/netlify-deploy-preview.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index da5ae89f5e..914161dad0 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -44,7 +44,6 @@ jobs:
         with:
           node-version: 20
           cache: 'npm'
-          cache-dependency-path: ./website/package-lock.json
 
       - name: Install npm deps
         run: npm ci
@@ -85,7 +84,6 @@ jobs:
         with:
           node-version: 20
           cache: 'npm'
-          cache-dependency-path: ./website/package-lock.json
 
       - name: Install npm deps
         run: npm ci

From 71a1b0d463efbfbab511793f0d2ecd8a5d3b7da4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 12:48:33 +0200
Subject: [PATCH 20/21] don't set wkdir

---
 .github/workflows/netlify-deploy-preview.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 914161dad0..4157b8076c 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -28,9 +28,6 @@ jobs:
   deploy-main-site:
     name: 'Deploy preview for main-site'
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: website
     needs: change-detection
     if: github.repository == 'nf-core/website' && needs.change-detection.outputs.main-site_any_changed == 'true'
     permissions:
@@ -68,9 +65,6 @@ jobs:
   deploy-docs:
     name: 'Deploy preview for docs'
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: website
     needs: change-detection
     if: github.repository == 'nf-core/website' && needs.change-detection.outputs.docs_any_changed == 'true'
     permissions:

From 92d3af727ef5b6b9e28927ac00a69e9fc679305b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 3 Jul 2024 13:00:29 +0200
Subject: [PATCH 21/21] retrigger build

---
 .github/workflows/netlify-deploy-preview.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/netlify-deploy-preview.yml b/.github/workflows/netlify-deploy-preview.yml
index 4157b8076c..7cb0f010bb 100644
--- a/.github/workflows/netlify-deploy-preview.yml
+++ b/.github/workflows/netlify-deploy-preview.yml
@@ -81,6 +81,7 @@ jobs:
 
       - name: Install npm deps
         run: npm ci
+
       - name: Build website
         run: npm run build --workspace sites/docs