From fda6c42d86d8d2466cc221b4eae306c03eaf365b Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 1 Apr 2026 12:03:45 +0200 Subject: [PATCH 1/5] test esm version of setup-nf-test --- .github/workflows/create-test-lint-wf-template.yml | 2 +- .github/workflows/create-test-wf.yml | 2 +- .github/workflows/pytest.yml | 2 +- .github/workflows/update-template-snapshots.yml | 2 +- nf_core/pipeline-template/.github/actions/get-shards/action.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 564f5b2621..05b8882d51 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -77,7 +77,7 @@ jobs: version: latest-everything - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps # TODO: revert to v1 after nf-core/setup-nf-test#32 is merged with: version: "0.9.4" install-pdiff: true diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 90dba2583a..bf35305696 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -63,7 +63,7 @@ jobs: version: ${{ matrix.NXF_VER }} - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps with: version: "0.9.4" install-pdiff: true diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 45d5422b69..d722e238e2 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -95,7 +95,7 @@ jobs: uses: nf-core/setup-nextflow@v2 - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps - name: move coveragerc file up run: | diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml index 05e07632e8..d2e280988e 100644 --- a/.github/workflows/update-template-snapshots.yml +++ b/.github/workflows/update-template-snapshots.yml @@ -74,7 +74,7 @@ jobs: version: latest-everything - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps with: version: "0.9.4" install-pdiff: true diff --git a/nf_core/pipeline-template/.github/actions/get-shards/action.yml b/nf_core/pipeline-template/.github/actions/get-shards/action.yml index d2f98f85fd..c3f4f6e4d7 100644 --- a/nf_core/pipeline-template/.github/actions/get-shards/action.yml +++ b/nf_core/pipeline-template/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps with: version: ${{ env.NFT_VER }} - name: Get number of shards From ee9fc08c3f687bef86f9748f8f9efa7e2c6fe8bc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Wed, 1 Apr 2026 13:23:00 +0200 Subject: [PATCH 2/5] Apply suggestion from @mashehu --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 05b8882d51..2d3afc2d35 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -77,7 +77,7 @@ jobs: version: latest-everything - name: Install nf-test - uses: nf-core/setup-nf-test@update-deps # TODO: revert to v1 after nf-core/setup-nf-test#32 is merged + uses: nf-core/setup-nf-test@update-deps with: version: "0.9.4" install-pdiff: true From 2478908c37d7526281f44857d4a503c2e1739a0b Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 1 Apr 2026 12:03:45 +0200 Subject: [PATCH 3/5] test esm version of setup-nf-test --- .github/workflows/create-test-lint-wf-template.yml | 2 +- .github/workflows/create-test-wf.yml | 2 +- .github/workflows/pytest.yml | 2 +- .github/workflows/update-template-snapshots.yml | 2 +- nf_core/pipeline-template/.github/actions/get-shards/action.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 564f5b2621..05b8882d51 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -77,7 +77,7 @@ jobs: version: latest-everything - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps # TODO: revert to v1 after nf-core/setup-nf-test#32 is merged with: version: "0.9.4" install-pdiff: true diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 90dba2583a..bf35305696 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -63,7 +63,7 @@ jobs: version: ${{ matrix.NXF_VER }} - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps with: version: "0.9.4" install-pdiff: true diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 45d5422b69..d722e238e2 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -95,7 +95,7 @@ jobs: uses: nf-core/setup-nextflow@v2 - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps - name: move coveragerc file up run: | diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml index 05e07632e8..d2e280988e 100644 --- a/.github/workflows/update-template-snapshots.yml +++ b/.github/workflows/update-template-snapshots.yml @@ -74,7 +74,7 @@ jobs: version: latest-everything - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps with: version: "0.9.4" install-pdiff: true diff --git a/nf_core/pipeline-template/.github/actions/get-shards/action.yml b/nf_core/pipeline-template/.github/actions/get-shards/action.yml index d2f98f85fd..c3f4f6e4d7 100644 --- a/nf_core/pipeline-template/.github/actions/get-shards/action.yml +++ b/nf_core/pipeline-template/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@update-deps with: version: ${{ env.NFT_VER }} - name: Get number of shards From 83b5fb3225d7f331d1f0addd8d496e46f800e255 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 1 Apr 2026 16:51:03 +0200 Subject: [PATCH 4/5] test new setup-nextflow --- .github/actions/create-lint-wf/action.yml | 2 +- .github/workflows/create-test-lint-wf-template.yml | 2 +- .github/workflows/create-test-wf.yml | 2 +- .github/workflows/pytest.yml | 2 +- .github/workflows/sync.yml | 2 +- .github/workflows/update-template-snapshots.yml | 2 +- nf_core/pipeline-template/.github/actions/nf-test/action.yml | 2 +- .../pipeline-template/.github/workflows/download_pipeline.yml | 2 +- nf_core/pipeline-template/.github/workflows/linting.yml | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index 307f153fbb..a36580ee31 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -16,7 +16,7 @@ runs: export NXF_WORK=$(pwd) - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 with: version: ${{ matrix.NXF_VER }} diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 05b8882d51..3aa233bc9e 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -72,7 +72,7 @@ jobs: run: uv sync --all-extras - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 with: version: latest-everything diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index bf35305696..0364c1d0c2 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -58,7 +58,7 @@ jobs: run: uv sync - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 with: version: ${{ matrix.NXF_VER }} diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index d722e238e2..572e3ec5dd 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -92,7 +92,7 @@ jobs: run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 - name: Install nf-test uses: nf-core/setup-nf-test@update-deps diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index b84b541523..8b4f16b67e 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -90,7 +90,7 @@ jobs: run: uv sync - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 with: version: "latest-everything" diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml index d2e280988e..6046be5524 100644 --- a/.github/workflows/update-template-snapshots.yml +++ b/.github/workflows/update-template-snapshots.yml @@ -69,7 +69,7 @@ jobs: run: uv sync --all-extras - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 with: version: latest-everything diff --git a/nf_core/pipeline-template/.github/actions/nf-test/action.yml b/nf_core/pipeline-template/.github/actions/nf-test/action.yml index a9f33909e6..05b9762e01 100644 --- a/nf_core/pipeline-template/.github/actions/nf-test/action.yml +++ b/nf_core/pipeline-template/.github/actions/nf-test/action.yml @@ -20,7 +20,7 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 with: version: "{% raw %}${{ env.NXF_VERSION }}" diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index bedd6f482b..8a5496d50d 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -39,7 +39,7 @@ jobs: needs: configure steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 63b9327097..da89f3aa38 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -23,7 +23,7 @@ jobs: uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@mashehu-patch-1 - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: From 0461e4dec1a3c3970d101e8845723d531ee57a99 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 8 Apr 2026 11:12:51 +0200 Subject: [PATCH 5/5] switch to master branch for setup-nextflow --- .github/actions/create-lint-wf/action.yml | 2 +- .github/workflows/create-test-lint-wf-template.yml | 2 +- .github/workflows/create-test-wf.yml | 2 +- .github/workflows/pytest.yml | 2 +- .github/workflows/sync.yml | 2 +- .github/workflows/update-template-snapshots.yml | 2 +- nf_core/pipeline-template/.github/actions/nf-test/action.yml | 2 +- .../pipeline-template/.github/workflows/download_pipeline.yml | 2 +- nf_core/pipeline-template/.github/workflows/linting.yml | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index a36580ee31..82abc4c264 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -16,7 +16,7 @@ runs: export NXF_WORK=$(pwd) - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master with: version: ${{ matrix.NXF_VER }} diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 62fd3805d4..59b62d083f 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -72,7 +72,7 @@ jobs: run: uv sync --all-extras - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master with: version: latest-everything diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index d77a8bc018..0d187ee56b 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -58,7 +58,7 @@ jobs: run: uv sync - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master with: version: ${{ matrix.NXF_VER }} diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 9af8b252b2..15ed61675f 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -92,7 +92,7 @@ jobs: run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master - name: Install nf-test uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2 diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index 8b4f16b67e..abdf449739 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -90,7 +90,7 @@ jobs: run: uv sync - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master with: version: "latest-everything" diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml index 8ef1e40272..fe30891044 100644 --- a/.github/workflows/update-template-snapshots.yml +++ b/.github/workflows/update-template-snapshots.yml @@ -69,7 +69,7 @@ jobs: run: uv sync --all-extras - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master with: version: latest-everything diff --git a/nf_core/pipeline-template/.github/actions/nf-test/action.yml b/nf_core/pipeline-template/.github/actions/nf-test/action.yml index 21b8541ded..8eb85b4f17 100644 --- a/nf_core/pipeline-template/.github/actions/nf-test/action.yml +++ b/nf_core/pipeline-template/.github/actions/nf-test/action.yml @@ -20,7 +20,7 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master with: version: "{% raw %}${{ env.NXF_VERSION }}" diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 8a5496d50d..62f5e9e873 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -39,7 +39,7 @@ jobs: needs: configure steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index da89f3aa38..0365515f3c 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -23,7 +23,7 @@ jobs: uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - name: Install Nextflow - uses: nf-core/setup-nextflow@mashehu-patch-1 + uses: nf-core/setup-nextflow@master - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: