From e064b76a7f4d2d5b41d10976400101ac83a18498 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Wed, 28 Feb 2024 13:48:48 +0000 Subject: [PATCH 1/3] Unpin pinned dependecies for tower actions --- nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 4 ++-- nf_core/pipeline-template/.github/workflows/awstest.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index 6121942ca1..4c9fd69fcc 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@aa88624706d400097880b69f1204f7f25436e93f # v2 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters {%- raw %} @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml index 0f775d783b..25726aa1c9 100644 --- a/nf_core/pipeline-template/.github/workflows/awstest.yml +++ b/nf_core/pipeline-template/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action {%- raw %} - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@aa88624706d400097880b69f1204f7f25436e93f # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | From c6bc426a4d96fa81d3a5c7c6ea8ea3fc71596554 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 28 Feb 2024 13:51:47 +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 3fe084d81a..6d7730dfe2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ - chore(deps): update seqeralabs/action-tower-launch digest to aa88624 ([#2793](https://github.com/nf-core/tools/pull/2793)) - chore(deps): update codecov/codecov-action digest to 0cfda1d ([#2794](https://github.com/nf-core/tools/pull/2794)) - chore(deps): update gitpod/workspace-base docker digest to c15ee2f ([#2799](https://github.com/nf-core/tools/pull/2799)) +- Unpin dependencies ([#2806](https://github.com/nf-core/tools/pull/2806)) ## [v2.13 - Tin Puppy](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-20] From 3725453013905d2aeb527a3260a30dd39533261e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 29 Feb 2024 13:06:41 +0000 Subject: [PATCH 3/3] unpin 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/rich-codex.yml | 2 +- .github/workflows/sync.yml | 2 +- nf_core/pipeline-template/.github/workflows/ci.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 3b63f198cc..51bf2ae5f7 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -17,7 +17,7 @@ runs: # Set up Nextflow - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 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 6f27236462..188cccfd75 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -72,7 +72,7 @@ jobs: pip install . - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: latest-everything diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 0166931be7..cd36d4e62d 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -59,7 +59,7 @@ jobs: pip install . - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: ${{ matrix.NXF_VER }} diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 5faeef49da..da7d267b7b 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -113,7 +113,7 @@ jobs: run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - name: Look if nf-test is already installed and write to env variable id: check-nftest diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml index 0e8a1c5e9b..8748f3d7b3 100644 --- a/.github/workflows/rich-codex.yml +++ b/.github/workflows/rich-codex.yml @@ -15,7 +15,7 @@ jobs: cache-dependency-path: setup.py - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - name: Cache nf-test installation id: cache-software diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index d89e255bfb..c998552ddd 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -67,7 +67,7 @@ jobs: pip install . - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "latest-everything" diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index 631862d9ec..84c727f60d 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}" diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 20b811ab2b..dcd7caabfc 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 3ec259b5ed..59b85f95fc 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: