From 86926c54c8cbd0c05199a753406639a8b63aa238 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 1 Feb 2024 11:06:29 +0100 Subject: [PATCH 1/3] Revert "Pin dependencies" This reverts commit f287057425c24ce09f0afad67ddcac8468e1fd70. # Conflicts: # .github/workflows/pytest.yml --- .github/workflows/branch.yml | 2 +- .github/workflows/changelog.yml | 6 +++--- .github/workflows/clean-up.yml | 2 +- .github/workflows/create-lint-wf.yml | 8 ++++---- .../workflows/create-test-lint-wf-template.yml | 8 ++++---- .github/workflows/create-test-wf.yml | 8 ++++---- .github/workflows/deploy-pypi.yml | 4 ++-- .github/workflows/lint-code.yml | 4 ++-- .github/workflows/push_dockerhub_dev.yml | 2 +- .github/workflows/push_dockerhub_release.yml | 2 +- .github/workflows/pytest.yml | 16 ++++++++-------- .github/workflows/rich-codex.yml | 8 ++++---- .github/workflows/sync.yml | 10 +++++----- .github/workflows/tools-api-docs-dev.yml | 6 +++--- .github/workflows/tools-api-docs-release.yml | 6 +++--- Dockerfile | 2 +- nf_core/gitpod/gitpod.Dockerfile | 2 +- .../.github/workflows/awsfulltest.yml | 4 ++-- .../.github/workflows/awstest.yml | 4 ++-- .../.github/workflows/branch.yml | 2 +- .../pipeline-template/.github/workflows/ci.yml | 4 ++-- .../.github/workflows/clean-up.yml | 2 +- .../.github/workflows/download_pipeline.yml | 6 +++--- .../.github/workflows/linting.yml | 12 ++++++------ .../.github/workflows/linting_comment.yml | 4 ++-- .../.github/workflows/release-announcements.yml | 4 ++-- 26 files changed, 69 insertions(+), 69 deletions(-) diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 7e3b30a836..54dee6df16 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -18,7 +18,7 @@ jobs: # If the above check failed, post a comment on the PR explaining the failure - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@7c0890544fb33b0bdd2e59467fbacb62e028a096 # v2 + uses: mshick/add-pr-comment@v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index 6316d62f33..63dcf2e428 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -17,7 +17,7 @@ jobs: ) steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 with: token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} @@ -34,7 +34,7 @@ jobs: fi gh pr checkout $PR_NUMBER - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@v5 with: python-version: "3.11" @@ -63,7 +63,7 @@ jobs: echo "File changed: ${{ env.changed }}" - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 cache: "pip" diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index a9cd4e930c..ff311f9df8 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 + - uses: actions/stale@v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index f41e9b0f5e..c4d0358982 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -42,12 +42,12 @@ jobs: export NXF_WORK=$(pwd) # Get the repo code - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out source-code repository # Set up nf-core/tools - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 cache: pip @@ -59,7 +59,7 @@ jobs: # Set up Nextflow - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 with: version: ${{ matrix.NXF_VER }} @@ -147,7 +147,7 @@ jobs: - name: Upload log file artifact if: ${{ always() }} - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4 + uses: actions/upload-artifact@v4 with: name: nf-core-log-file-${{ matrix.NXF_VER }} path: create-lint-wf/log.txt diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 9a5519cb93..7d586fc3d2 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -57,11 +57,11 @@ jobs: cd create-lint-wf-template export NXF_WORK=$(pwd) - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out source-code repository - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 @@ -71,7 +71,7 @@ jobs: pip install . - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 with: version: latest-everything @@ -154,7 +154,7 @@ jobs: - name: Upload log file artifact if: ${{ always() }} - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4 + uses: actions/upload-artifact@v4 with: name: nf-core-log-file-${{ matrix.TEMPLATE }} path: create-test-lint-wf/artifact_files.tar diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index f1809086c5..9301d1224e 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -41,11 +41,11 @@ jobs: cd create-test-wf export NXF_WORK=$(pwd) - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out source-code repository - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 @@ -55,7 +55,7 @@ jobs: pip install . - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 with: version: ${{ matrix.NXF_VER }} @@ -68,7 +68,7 @@ jobs: - name: Upload log file artifact if: ${{ always() }} - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4 + uses: actions/upload-artifact@v4 with: name: nf-core-log-file-${{ matrix.NXF_VER }} path: create-test-wf/log.txt diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml index e53d2f2f5a..8d3a154d80 100644 --- a/.github/workflows/deploy-pypi.yml +++ b/.github/workflows/deploy-pypi.yml @@ -13,11 +13,11 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out source-code repository - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index 8ed52a0582..d9847dd365 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -18,10 +18,10 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 cache: "pip" diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml index af11a79990..169a917d83 100644 --- a/.github/workflows/push_dockerhub_dev.yml +++ b/.github/workflows/push_dockerhub_dev.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@v4 - name: Build nfcore/tools:dev docker image run: docker build --no-cache . -t nfcore/tools:dev diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml index 0b3f381d86..49ce17dd84 100644 --- a/.github/workflows/push_dockerhub_release.yml +++ b/.github/workflows/push_dockerhub_release.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@v4 - name: Build nfcore/tools:latest docker image run: docker build --no-cache . -t nfcore/tools:latest diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index ff4415d30a..12c8a34000 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -58,7 +58,7 @@ jobs: name: Get test file matrix runs-on: "ubuntu-latest" steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out source-code repository - name: List tests @@ -83,11 +83,11 @@ jobs: cd pytest export NXF_WORK=$(pwd) - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out source-code repository - name: Set up Python ${{ needs.setup.outputs.python-version }} - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: ${{ needs.setup.outputs.python-version }} cache: "pip" @@ -111,7 +111,7 @@ jobs: run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 - name: Look if nf-test is already installed and write to env variable id: check-nftest @@ -155,7 +155,7 @@ jobs: fi - name: Upload coverage - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4 + uses: actions/upload-artifact@v4 with: name: coverage_${{ matrix.test }} path: .coverage @@ -169,9 +169,9 @@ jobs: mkdir -p pytest cd pytest - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 env: AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/ with: @@ -188,7 +188,7 @@ jobs: mv .github/.coveragerc . - name: Download all artifacts - uses: actions/download-artifact@6b208ae046db98c579e8a3aa621ab581ff575935 # v4 + uses: actions/download-artifact@v4 - name: Run coverage run: | coverage combine --keep coverage*/.coverage* diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml index 030b11c790..ecbae8ffec 100644 --- a/.github/workflows/rich-codex.yml +++ b/.github/workflows/rich-codex.yml @@ -6,16 +6,16 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repo - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.x cache: pip cache-dependency-path: setup.py - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 - name: Cache nf-test installation id: cache-software @@ -36,7 +36,7 @@ jobs: run: pip install git+https://github.com/nf-core/tools.git@dev - name: Generate terminal images with rich-codex - uses: ewels/rich-codex@8ce988cc253c240a3027ba58e33e47640935dd8b # v1 + uses: ewels/rich-codex@v1 env: COLUMNS: 100 HIDE_PROGRESS: "true" diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index ba4c16531e..aeb24839f1 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -43,10 +43,10 @@ jobs: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out nf-core/tools - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 name: Check out nf-core/${{ matrix.pipeline }} with: repository: nf-core/${{ matrix.pipeline }} @@ -56,7 +56,7 @@ jobs: fetch-depth: "0" - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 @@ -66,7 +66,7 @@ jobs: pip install . - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 with: version: "latest-everything" @@ -85,7 +85,7 @@ jobs: - name: Upload sync log file artifact if: ${{ always() }} - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4 + uses: actions/upload-artifact@v4 with: name: sync_log_${{ matrix.pipeline }} path: sync_log_${{ matrix.pipeline }}.txt diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml index 19a1621092..91396b2a25 100644 --- a/.github/workflows/tools-api-docs-dev.yml +++ b/.github/workflows/tools-api-docs-dev.yml @@ -24,10 +24,10 @@ jobs: steps: - name: Check out source-code repository - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@v4 - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 @@ -43,7 +43,7 @@ jobs: - name: Sync dev docs # Only sync with the website if it was a push from nf-core/tools dev branch if: github.repository == 'nf-core/tools' && github.event_name == 'push' && github.event.ref == 'refs/heads/dev' - uses: SamKirkland/FTP-Deploy-Action@8a24039354ee91000cb948cb4a1dbdf1a1b94a3c # v4.3.4 + uses: SamKirkland/FTP-Deploy-Action@v4.3.4 with: server: ${{ secrets.ftp_server }} username: ${{ secrets.ftp_username}} diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml index 45ce237f13..2183db3fcf 100644 --- a/.github/workflows/tools-api-docs-release.yml +++ b/.github/workflows/tools-api-docs-release.yml @@ -19,10 +19,10 @@ jobs: - ${{ github.event.release.tag_name }} steps: - name: Check out source-code repository - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@v4 - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 @@ -37,7 +37,7 @@ jobs: - name: Sync release docs if: github.repository == 'nf-core/tools' - uses: SamKirkland/FTP-Deploy-Action@8a24039354ee91000cb948cb4a1dbdf1a1b94a3c # v4.3.4 + uses: SamKirkland/FTP-Deploy-Action@v4.3.4 with: server: ${{ secrets.ftp_server }} username: ${{ secrets.ftp_username}} diff --git a/Dockerfile b/Dockerfile index dd7b1889fc..9c9770c25f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.11-slim@sha256:d11b9bd5e49ea7401753d78f4d3b56f3aec952b85b49bcae88981f0452818e0b +FROM python:3.11-slim LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for the nfcore tools" diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 27ab60127f..ad4bed5052 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -1,7 +1,7 @@ # Test build locally before making a PR # docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile . -FROM gitpod/workspace-base@sha256:7a130ed80741c3f838a7607f88296d26ac477e713c12b638ab93874d3169f7f1 +FROM gitpod/workspace-base USER root diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index ef0499dc35..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@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # 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@26f96dfa697d77e81fd5907df203aa23a56210a8 # 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 c4f0e3a2fd..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@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/nf_core/pipeline-template/.github/workflows/branch.yml b/nf_core/pipeline-template/.github/workflows/branch.yml index 6cac19027e..057016e4be 100644 --- a/nf_core/pipeline-template/.github/workflows/branch.yml +++ b/nf_core/pipeline-template/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@7c0890544fb33b0bdd2e59467fbacb62e028a096 # v2 + uses: mshick/add-pr-comment@v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index e441326f6e..3edd49f09d 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -28,10 +28,10 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 with: version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}" diff --git a/nf_core/pipeline-template/.github/workflows/clean-up.yml b/nf_core/pipeline-template/.github/workflows/clean-up.yml index b3b5c05d60..8feb3fb017 100644 --- a/nf_core/pipeline-template/.github/workflows/clean-up.yml +++ b/nf_core/pipeline-template/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 + - uses: actions/stale@v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 1aff7a8fc1..07ac82c1ed 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -23,13 +23,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@v5 with: python-version: "3.11" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + - uses: eWaterCycle/setup-singularity@v7 with: singularity-version: 3.8.3 diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index c748a3ab28..a267f1ec14 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@v4 - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + uses: actions/setup-python@v5 with: python-version: 3.11 cache: "pip" @@ -32,12 +32,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1 + uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@v5 with: python-version: "3.11" architecture: "x64" @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4 + uses: actions/upload-artifact@v4 with: name: linting-logs path: | diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml index 0c030650cb..e5528b29cf 100644 --- a/nf_core/pipeline-template/.github/workflows/linting_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@e7466d1a7587ed14867642c2ca74b5bcc1e19a2d # v3 + uses: dawidd6/action-download-artifact@v3 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@efaaab3fd41a9c3de579aba759d2552635e590fd # v2 + uses: marocchino/sticky-pull-request-comment@v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/nf_core/pipeline-template/.github/workflows/release-announcements.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml index f293032771..1dd48b123f 100644 --- a/nf_core/pipeline-template/.github/workflows/release-announcements.yml +++ b/nf_core/pipeline-template/.github/workflows/release-announcements.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +56,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 + - uses: zentered/bluesky-post-action@v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! From 6ffb9e364f56084b226d291c3e76642bed118b6b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 1 Feb 2024 10:08:25 +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 18ee087433..7a3e750aa2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ - fix changelog titles ([#2708](https://github.com/nf-core/tools/pull/2708)) - Print relative path not absolute path in logo cmd log output ([#2709](https://github.com/nf-core/tools/pull/2709)) - Update codecov/codecov-action action to v4 ([#2713](https://github.com/nf-core/tools/pull/2713)) +- Revert pin dependency ([#2719](https://github.com/nf-core/tools/pull/2719)) ## [v2.12 - Aluminium Wolf](https://github.com/nf-core/tools/releases/tag/2.11) - [2024-01-29] From 0382956815d269f5bf3af8562bde5362dd813448 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 1 Feb 2024 10:23:27 +0000 Subject: [PATCH 3/3] update CHANGELOG --- CHANGELOG.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d5d0bd2d2e..70cf2de07a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,17 +2,11 @@ ## [v2.12.1 - Aluminium Wolf - Patch](https://github.com/nf-core/tools/releases/tag/2.12.1) - [2024-02-01] -### Template - ### Linting - Handle default values of type number from nextflow schema ([#2703](https://github.com/nf-core/tools/pull/2703)) - fix ignoring files_unchanged ([#2707](https://github.com/nf-core/tools/pull/2707)) -### Modules - -### Subworkflows - ### General - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15 ([#2705](https://github.com/nf-core/tools/pull/2705))