From 61ad31d6f8b05344aa1e00a92807839e3329c93e Mon Sep 17 00:00:00 2001 From: Valentin Schneider-Lunitz Date: Fri, 24 Apr 2026 08:41:13 +0000 Subject: [PATCH 1/2] docs(tutorials): update crypt4GH to proTES guide Signed-off-by: Valentin Schneider-Lunitz --- docs/tutorials/crypt4gh_to_protes.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/tutorials/crypt4gh_to_protes.md b/docs/tutorials/crypt4gh_to_protes.md index 44d8376..4eeb27c 100644 --- a/docs/tutorials/crypt4gh_to_protes.md +++ b/docs/tutorials/crypt4gh_to_protes.md @@ -169,6 +169,8 @@ funnel server run --config server-config.yaml & ```bash cd funnel +# If worker terminates after one task execution, put the command in a while loop. +# while true; do funnel node run --config worker-config.yaml; done funnel node run --config worker-config.yaml & ``` @@ -176,9 +178,9 @@ Verify that both services are running by checking the logs or accessing the Funn ### Step 5: Configure ProTES -ProTES acts as a gateway and provides middleware for automatic Crypt4GH decryption. Follow the [proTES](https://github.com/elixir-cloud-aai/proTES) installation guide to deploy proTES on your third VM. +ProTES acts as a gateway and provides middleware for automatic Crypt4GH decryption. Follow the [proTES](https://github.com/elixir-cloud-aai/proTES) (use 'adjust_middleware' branch if not yet merged) installation guide to deploy proTES on your third VM. -For detailed middleware installation, refer to the [protes-middleware-crypt4gh](https://github.com/elixir-cloud-aai/protes-middleware-crypt4gh). +For detailed middleware installation, refer to the [protes-middleware-crypt4gh](https://github.com/elixir-cloud-aai/protes-middleware-crypt4gh) (use 'update_middleware' branch if not yet merged). Once installed, configure the Crypt4GH middleware by editing the `pro_tes/config.yaml` file: From c07d48d5737b07acecf76b8ce88068cbda6f7d1e Mon Sep 17 00:00:00 2001 From: Sven Twardziok Date: Mon, 6 Jul 2026 08:38:45 +0200 Subject: [PATCH 2/2] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- docs/tutorials/crypt4gh_to_protes.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/tutorials/crypt4gh_to_protes.md b/docs/tutorials/crypt4gh_to_protes.md index 4eeb27c..9f0ede3 100644 --- a/docs/tutorials/crypt4gh_to_protes.md +++ b/docs/tutorials/crypt4gh_to_protes.md @@ -178,9 +178,11 @@ Verify that both services are running by checking the logs or accessing the Funn ### Step 5: Configure ProTES -ProTES acts as a gateway and provides middleware for automatic Crypt4GH decryption. Follow the [proTES](https://github.com/elixir-cloud-aai/proTES) (use 'adjust_middleware' branch if not yet merged) installation guide to deploy proTES on your third VM. +ProTES acts as a gateway and provides middleware for automatic Crypt4GH decryption. Follow the [proTES](https://github.com/elixir-cloud-aai/proTES) installation guide to deploy proTES on your third VM. -For detailed middleware installation, refer to the [protes-middleware-crypt4gh](https://github.com/elixir-cloud-aai/protes-middleware-crypt4gh) (use 'update_middleware' branch if not yet merged). +For detailed middleware installation, refer to the [protes-middleware-crypt4gh](https://github.com/elixir-cloud-aai/protes-middleware-crypt4gh) repository. + +**Note:** If the branch-specific changes are not yet merged, use the `adjust_middleware` branch for `proTES` and the `update_middleware` branch for `protes-middleware-crypt4gh`. Once those changes are merged, use each repository's default branch. Once installed, configure the Crypt4GH middleware by editing the `pro_tes/config.yaml` file: