From 38a98ed11a747f682874dbee3dd2d455c76a7376 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Jul 2026 12:23:56 +0200
Subject: [PATCH 1/2] add nextflow version fallback to handle pipelines with
 strict and non-strict syntax in sync action

---
 .github/workflows/sync.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index e62b7a4869..7d9cf05901 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -108,7 +108,31 @@ jobs:
           git config --global init.defaultBranch $defaultBranch
 
       - name: Run synchronisation
+        id: sync
         if: github.repository == 'nf-core/tools'
+        continue-on-error: true
+        env:
+          GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+        run: |
+          git config --global user.email "core@nf-co.re"
+          git config --global user.name "nf-core-bot"
+          uv run nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
+            ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }} \
+            pipelines sync -d nf-core/${{ matrix.pipeline }} \
+            --from-branch dev \
+            --pull-request \
+            --username nf-core-bot \
+            --github-repository nf-core/${{ matrix.pipeline }} \
+            --blog-post ${{inputs.blog_post}}
+
+      - name: Install newer Nextflow (retry fallback)
+        if: github.repository == 'nf-core/tools' && steps.sync.outcome == 'failure'
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
+        with:
+          version: "26.04.6"
+
+      - name: Retry synchronisation with newer Nextflow
+        if: github.repository == 'nf-core/tools' && steps.sync.outcome == 'failure'
         env:
           GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
         run: |

From eb5028dfd174251b3dd08f513b1d317c73ec2090 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Jul 2026 12:25:34 +0200
Subject: [PATCH 2/2] catch traceback if nextflow config command fails

---
 nf_core/utils.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index e53744bb88..93a09971ba 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -553,7 +553,12 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
     log.debug("No config cache found")
 
     # Call `nextflow config`
-    result = run_cmd("nextflow", f"config -o json {wf_path}")
+    try:
+        result = run_cmd("nextflow", f"config -o json {wf_path}")
+    except RuntimeError as e:
+        raise UserWarning(
+            f"Could not parse Nextflow config for '{wf_path}'. Possibly because of a Nextflow version mismatch?\n{e}"
+        ) from e
     if result is not None:
         nfconfig_raw, _ = result
         try: