From 9fad0213a5d22efe2300958ae16fdd578a13abe4 Mon Sep 17 00:00:00 2001 From: Shijie Zheng Date: Tue, 23 Sep 2025 15:23:21 -0400 Subject: [PATCH 1/3] Fix: Add NXF_VERSION environment variable to nf-test workflow - Add NXF_VERSION: ${{ matrix.NXF_VER }} to env section in nf-test step - This fixes the missing environment variable that .github/actions/nf-test expects - The nf-test action uses ${{ env.NXF_VERSION }} for Nextflow setup but it wasn't being passed from the workflow --- nf_core/pipeline-template/.github/workflows/nf-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index 4a108cc4fb..21df44a1b9 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -97,6 +97,7 @@ jobs: continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + NXF_VERSION: ${{ matrix.NXF_VER }} with: profile: ${{ matrix.profile }} shard: ${{ matrix.shard }} From b1ccfe982dd5ca04f3f5c117e24d34198ce3c1dd Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 24 Sep 2025 11:56:31 +0000 Subject: [PATCH 2/3] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bab0ac910b..2faed13ada 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -47,6 +47,7 @@ - Fix backwards compatibility with python 3.9 in use of Enum ([#3736](https://github.com/nf-core/tools/pull/3736)) - Fix downloads: temporary files not moved and cleaned up correctly after singularity pull ([#3749](https://github.com/nf-core/tools/pull/3749)) - impr devcontainer: Add hostRequirements to run with 4CPUs and 16GB ram by default ([#3746](https://github.com/nf-core/tools/pull/3746)) +- Fix: Add NXF_VERSION environment variable to nf-test workflow ([#3770](https://github.com/nf-core/tools/pull/3770)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 2ed23208e40b6f2cf4bc556e56ca30193e084a66 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 29 Sep 2025 13:33:27 +0000 Subject: [PATCH 3/3] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f515c881f8..b4603b6d19 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ - Bump minimum Nextflow version to 25.04.0 ([#3743](https://github.com/nf-core/tools/pull/3743)) - Explicitly declare conda-forge as a channel in the conda setup for GitHub CI for nf-test ([#3764](https://github.com/nf-core/tools/pull/3764)) - Update charliecloud URL ([#3757](https://github.com/nf-core/tools/pull/3757)) +- Fix: Add NXF_VERSION environment variable to nf-test workflow ([#3770](https://github.com/nf-core/tools/pull/3770)) ### Linting @@ -48,7 +49,6 @@ - Fix backwards compatibility with python 3.9 in use of Enum ([#3736](https://github.com/nf-core/tools/pull/3736)) - Fix downloads: temporary files not moved and cleaned up correctly after singularity pull ([#3749](https://github.com/nf-core/tools/pull/3749)) - impr devcontainer: Add hostRequirements to run with 4CPUs and 16GB ram by default ([#3746](https://github.com/nf-core/tools/pull/3746)) -- Fix: Add NXF_VERSION environment variable to nf-test workflow ([#3770](https://github.com/nf-core/tools/pull/3770)) - Add .nf-test/ to prettier ignore list ([#3776](https://github.com/nf-core/tools/pull/3776)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]