diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index b290e09..97c8c97 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,20 +1,20 @@ { "name": "nfcore", - "image": "nfcore/gitpod:latest", - "remoteUser": "gitpod", - "runArgs": ["--privileged"], + "image": "nfcore/devcontainer:latest", - // Configure tool-specific properties. - "customizations": { - // Configure properties specific to VS Code. - "vscode": { - // Set *default* container specific settings.json values on container create. - "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python" - }, + "remoteUser": "root", + "privileged": true, - // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } + "remoteEnv": { + // Workspace path on the host for mounting with docker-outside-of-docker + "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" + }, + + "onCreateCommand": "./.devcontainer/setup.sh", + + "hostRequirements": { + "cpus": 4, + "memory": "16gb", + "storage": "32gb" } } diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh new file mode 100755 index 0000000..85938c9 --- /dev/null +++ b/.devcontainer/setup.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +# Customise the terminal command prompt +echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc +echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc +export PROMPT_DIRTRIM=2 +export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' + +# Update Nextflow +nextflow self-update + +# Update welcome message +echo "Welcome to the nf-core/longraredisease devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index bf44d96..3b9724c 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -25,9 +25,9 @@ runs: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install nf-test uses: nf-core/setup-nf-test@v1 @@ -52,6 +52,8 @@ runs: with: auto-update-conda: true conda-solver: libmamba + channels: conda-forge + channel-priority: strict conda-remove-defaults: true - name: Run nf-test diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index a4c1d82..4eaf71e 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,48 @@ name: nf-core AWS full size tests -# This workflow is triggered on releases and pull-requests. -# It can be triggered manually with GitHub Actions workflow dispatch button. -# It runs the -profile test_full workflow with AWS Batch +# This workflow is triggered on PRs opened against the main/master branch. +# It can be additionally triggered manually with GitHub actions workflow dispatch button. +# It runs the -profile 'test_full' on AWS batch + on: - release: - types: [published] + workflow_dispatch: pull_request_review: types: [submitted] - workflow_dispatch: + release: + types: [published] jobs: run-platform: + name: Run AWS full tests + # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered + if: github.repository == 'nf-core/longraredisease' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release' runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - name: Run AWS full tests - run: echo "AWS full tests placeholder" + - name: Set revision variable + id: revision + run: | + echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" + + - name: Launch workflow via Seqera Platform + 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 + with: + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} + revision: ${{ steps.revision.outputs.revision }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/longraredisease/work-${{ steps.revision.outputs.revision }} + parameters: | + { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/longraredisease/results-${{ steps.revision.outputs.revision }}" + } + profiles: test_full + + - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + with: + name: Seqera Platform debug log file + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 69bb667..9440883 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -5,25 +5,29 @@ name: nf-core AWS test on: workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS tests - if: github.repository == 'fellen31/nallo' + if: github.repository == 'nf-core/longraredisease' runs-on: ubuntu-latest steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + # Launch workflow using Seqera Platform CLI tool action + - name: Launch workflow via Seqera Platform + uses: seqeralabs/action-tower-launch@v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nallo/work-${{ github.sha }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/longraredisease/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nallo/results-test-${{ github.sha }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/longraredisease/results-test-${{ github.sha }}" } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 + profiles: test + + - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: - name: Tower debug log file - path: tower_action_*.log + name: Seqera Platform debug log file + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 0b6b1f2..6adb0ff 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@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 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/download_pipeline.yml b/.github/workflows/download_pipeline.yml index ab06316..45884ff 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -12,14 +12,6 @@ on: required: true default: "dev" pull_request: - types: - - opened - - edited - - synchronize - branches: - - main - - master - pull_request_target: branches: - main - master @@ -52,9 +44,9 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.12" + python-version: "3.14" architecture: "x64" - name: Setup Apptainer @@ -65,7 +57,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git@dev + pip install git+https://github.com/nf-core/tools.git - name: Make a cache directory for the container images run: | @@ -120,6 +112,7 @@ jobs: echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts + id: count_comparison run: | if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} @@ -132,3 +125,10 @@ jobs: else echo "The pipeline can be downloaded successfully!" fi + + - name: Upload Nextflow logfile for debugging purposes + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + with: + name: nextflow_logfile.txt + path: .nextflow.log* + include-hidden-files: true diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml similarity index 75% rename from .github/workflows/fix-linting.yml rename to .github/workflows/fix_linting.yml index 8601eef..ac23801 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix_linting.yml @@ -9,17 +9,17 @@ jobs: if: > contains(github.event.comment.html_url, '/pull/') && contains(github.event.comment.body, '@nf-core-bot fix linting') && - github.repository == 'genomic-medicine-sweden/nallo' + github.repository == 'nf-core/longraredisease' runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} # indication that the linting is being fixed - name: React on comment - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: eyes @@ -32,9 +32,9 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.12" + python-version: "3.14" - name: Install pre-commit run: pip install pre-commit @@ -47,7 +47,7 @@ jobs: # indication that the linting has finished - name: react if linting finished succesfully if: steps.pre-commit.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: "+1" @@ -67,23 +67,23 @@ jobs: - name: react if linting errors were fixed id: react-if-fixed if: steps.commit-and-push.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: hooray - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: confused - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: issue-number: ${{ github.event.issue.number }} body: | @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. - See [CI log](https://github.com/genomic-medicine-sweden/nallo/actions/runs/${{ github.run_id }}) for more details. + See [CI log](https://github.com/nf-core/longraredisease/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8b0f88c..7a527a3 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,12 +11,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - - name: Set up Python 3.13 - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - name: Set up Python 3.14 + uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install pre-commit run: pip install pre-commit @@ -28,14 +28,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" architecture: "x64" - name: read .nf-core.yml @@ -71,7 +71,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index d43797d..e6e9bc2 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2 + uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 521b5e3..cfc58f2 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -1,12 +1,5 @@ -name: nf-test +name: Run nf-test on: - push: - paths-ignore: - - "docs/**" - - "**/meta.yml" - - "**/*.md" - - "**/*.png" - - "**/*.svg" pull_request: paths-ignore: - "docs/**" @@ -25,45 +18,65 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.2" + NFT_VER: "0.9.3" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity jobs: - find-tests: - runs-on: ubuntu-latest + nf-test-changes: + name: nf-test-changes + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test-changes + - runner=4cpu-linux-x64 outputs: - tags: ${{ steps.find.outputs.tags }} + shard: ${{ steps.set-shards.outputs.shard }} + total_shards: ${{ steps.set-shards.outputs.total_shards }} steps: - - uses: actions/checkout@v4 + - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner + run: | + ls -la ./ + rm -rf ./* || true + rm -rf ./.??* || true + ls -la ./ + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + with: + fetch-depth: 0 - - name: get subworkflows - id: find - uses: ./.github/actions/find-tests + - name: get number of shards + id: set-shards + uses: ./.github/actions/get-shards + env: + NFT_VER: ${{ env.NFT_VER }} + with: + max_shards: 7 - name: debug run: | - echo ${{ steps.find.outputs.tags }} + echo ${{ steps.set-shards.outputs.shard }} + echo ${{ steps.set-shards.outputs.total_shards }} nf-test: - name: "${{ matrix.tag }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }}" - needs: [find-tests] - runs-on: - - "ubuntu-latest" + name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" + needs: [nf-test-changes] + if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test + - runner=4cpu-linux-x64 strategy: fail-fast: false matrix: - profile: [docker, singularity] - tag: ${{ fromJson(needs.find-tests.outputs.tags) }} + shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} + profile: [conda, docker, singularity] isMain: - ${{ github.base_ref == 'master' || github.base_ref == 'main' }} + # Exclude conda and singularity on dev exclude: - isMain: false - profile: "singularity" + profile: "conda" - isMain: false - tag: "samplesheet_target_regions_null" + profile: "singularity" NXF_VER: - "25.04.6" - "latest-everything" @@ -72,38 +85,45 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: fetch-depth: 0 - - name: Clean up Disk space - if: startsWith(matrix.tag, 'samplesheet') - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - with: - android: true - dotnet: false - haskell: false - large-packages: false - docker-images: false - swap-storage: false - - name: Run nf-test + id: run_nf_test uses: ./.github/actions/nf-test + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + NXF_VERSION: ${{ matrix.NXF_VER }} with: profile: ${{ matrix.profile }} - tags: ${{ matrix.tag }} - shard: 1 - total_shards: 1 + shard: ${{ matrix.shard }} + total_shards: ${{ env.TOTAL_SHARDS }} + + - name: Report test status + if: ${{ always() }} + run: | + if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then + echo "::error::Test with ${{ matrix.NXF_VER }} failed" + # Add to workflow summary + echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY + if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then + echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." + fi + if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + exit 1 + fi + fi confirm-pass: needs: [nf-test] if: always() - runs-on: - - "ubuntu-latest" + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-confirm-pass + - runner=2cpu-linux-x64 steps: - - name: One or more tests failed + - name: One or more tests failed (excluding latest-everything) if: ${{ contains(needs.*.result, 'failure') }} run: exit 1 @@ -118,15 +138,7 @@ jobs: - name: debug-print if: always() run: | - echo "::group::DEBUG: \`needs\` Contents" + echo "::group::DEBUG: `needs` Contents" echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" echo "::endgroup::" - - - name: Clean Workspace - if: always() - run: | - ls -la ./ - rm -rf ./* || true - rm -rf ./.??* || true - ls -la ./ diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 76a9e67..431d3d4 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -14,6 +14,10 @@ jobs: run: | echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT + - name: get description + id: get_description + run: | + echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -22,7 +26,7 @@ jobs: # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release message: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - + ${{ steps.get_description.outputs.description }} Please see the changelog: ${{ github.event.release.html_url }} ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics @@ -30,7 +34,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 + - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml similarity index 91% rename from .github/workflows/template_version_comment.yml rename to .github/workflows/template-version-comment.yml index 537529b..e8560fc 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,12 +9,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: ref: ${{ github.event.pull_request.head.sha }} - name: Read template version from .nf-core.yml - uses: nichmor/minimal-read-yaml@v0.0.2 + uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml diff --git a/.gitignore b/.gitignore index e08b47f..a42ce01 100644 --- a/.gitignore +++ b/.gitignore @@ -7,29 +7,3 @@ testing/ testing* *.pyc null/ -node_modules/ -work/ -results/ -.nextflow -.nextflow.log -.nextflow.log.1 -.nextflow.log.2 -.nextflow.log.3 -.nextflow.log.4 -.nextflow.log.5 -.nextflow.log.6 -.nextflow.log.7 -.nextflow.log.8 -.nextflow.log.9 -dist/ -build/ -.venv/ -.mamba/ -.ruff_cache/ -.pytest_cache/ -node_modules/ -work/ -results/ -.nextflow* -dist/ -build/ diff --git a/.nf-core.yml b/.nf-core.yml index 4b0cb08..6b15064 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,18 +1,16 @@ -repository_type: pipeline - -nf_core_version: 3.3.2 - lint: template_strings: - - "assets/test_data/bam_pass/*.bam" - + - assets/test_data/bam_pass/*.bam +nf_core_version: 3.5.1 +repository_type: pipeline template: - org: nf-core - name: longraredisease - description: A Nextflow pipeline for rare disease diagnostics from Oxford Nanopore long-read sequencing data. Includes SV, SNV, CNV, and methylation profiling. author: Nour Mahfel - version: 1.0.0dev - force: true + description: A Nextflow pipeline for rare disease diagnostics from Oxford Nanopore + long-read sequencing data. Includes SV, SNV, CNV, and methylation profiling. + force: false + is_nfcore: true + name: longraredisease + org: nf-core outdir: . skip_features: [] - is_nfcore: true + version: 1.0.0 diff --git a/.nf-test.log b/.nf-test.log new file mode 100644 index 0000000..1382c05 --- /dev/null +++ b/.nf-test.log @@ -0,0 +1,18 @@ +Mar-24 17:25:03.915 [main] INFO com.askimed.nf.test.App - nf-test 0.9.4 +Mar-24 17:25:03.931 [main] INFO com.askimed.nf.test.App - Arguments: [test, tests/default.nf.test, --update-snapshot] +Mar-24 17:25:04.849 [main] INFO com.askimed.nf.test.App - Nextflow Version: 25.10.4 +Mar-24 17:25:04.850 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/nmahfel/nf-training/longraredisease/nf-test.config... +Mar-24 17:25:05.669 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 110 files from directory /home/nmahfel/nf-training/longraredisease in 0.191 sec +Mar-24 17:25:05.671 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests. +Mar-24 17:25:05.671 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/home/nmahfel/nf-training/longraredisease/tests/default.nf.test] +Mar-24 17:25:05.909 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute. +Mar-24 17:25:05.910 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan +Mar-24 17:25:05.910 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test pipeline' from file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test'. +Mar-24 17:25:05.911 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '461a1912: -profile test'. type: com.askimed.nf.test.lang.pipeline.PipelineTest +Mar-24 17:31:45.749 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test.snap' +Mar-24 17:31:45.761 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots '-profile test' do not match. Update snapshots flag set. +Mar-24 17:31:45.762 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot '-profile test' +Mar-24 17:31:45.764 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test.snap' +Mar-24 17:31:45.765 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '461a1912: -profile test' finished. status: PASSED +Mar-24 17:31:45.767 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test pipeline' finished. snapshot file: true, skipped tests: false, failed tests: false +Mar-24 17:31:45.769 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done! diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1dec865..d06777a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,10 +4,24 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.2.5 - - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.1.2" + - prettier@3.6.2 + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 hooks: - - id: editorconfig-checker - alias: ec + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/nf-core/.*| + subworkflows/nf-core/.*| + .*\.snap$ + )$ + - id: end-of-file-fixer + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/nf-core/.*| + subworkflows/nf-core/.*| + .*\.snap$ + )$ diff --git a/.prettierignore b/.prettierignore index edd29f0..dd749d4 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,4 +10,7 @@ testing/ testing* *.pyc bin/ +.nf-test/ ro-crate-metadata.json +modules/nf-core/ +subworkflows/nf-core/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 2a15a69..4111606 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,11 @@ -# nf-core/nanoraredx: Changelog +# nf-core/longraredisease: Changelog The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.0dev - [date] +## v1.0.0 - [date] -Initial release of nf-core/nanoraredx, created with the [nf-core](https://nf-co.re/) template. +Initial release of nf-core/longraredisease, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index 60f9401..8ccd82b 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# nf-core/nanoraredx: Citations +# nf-core/longraredisease: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) diff --git a/README.md b/README.md index 1b4c711..f47d173 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,17 @@

- + nf-core/longraredisease - +

-[![GitHub Actions CI Status](https://github.com/nf-core/longraredisease/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/longraredisease/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/longraredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/longraredisease/actions/workflows/linting.yml) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/longraredisease/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/longraredisease) +[![GitHub Actions CI Status](https://github.com/nf-core/longraredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/longraredisease/actions/workflows/nf-test.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/longraredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/longraredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/longraredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A525.04.0-23aa62.svg)](https://www.nextflow.io/) -[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.6-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/longraredisease) @@ -61,7 +60,7 @@ The pipeline excels at identifying and interpreting structural variants through: ### Software -- **Nextflow** ≥25.04.0 (DSL2) +- **Nextflow** ≥25.04.6 (DSL2) - **Container engine:** Docker, Singularity/Apptainer, or Podman - **Java** ≥17 (required by Nextflow) @@ -84,7 +83,7 @@ The pipeline excels at identifying and interpreting structural variants through: ### 1. Install Nextflow ```bash -# Install Nextflow (≥25.04.0) +# Install Nextflow (≥25.04.6) curl -s https://get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 2fc65dd..f8b42ee 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -1,4 +1,3 @@ -content: id: "nf-core-longraredisease-methods-description" description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." section_name: "nf-core/longraredisease Methods Description" @@ -25,7 +24,6 @@ data: |
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • ${tool_bibliography} -
    Notes: