Merge branch 'dev' into enhancement/cancer-type-parameter-reporting

.github/workflows/awsfulltest.yml

@@ -1,18 +1,35 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the 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]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/oncoanalyser'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == 'nf-core/oncoanalyser' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
+      - uses: octokit/[email protected]
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required

.github/workflows/ci.yml

@@ -7,37 +7,79 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   test:
-    name: Run pipeline stubs
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/oncoanalyser') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test_stub"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
+
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline stubs only
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -stub -profile test_stub --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -stub -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results

.github/workflows/download_pipeline.yml

@@ -1,4 +1,4 @@
-name: Test successful pipeline download with 'nf-core download'
+name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
     inputs:
       testbranch:
-        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
         required: true
         default: "dev"
   pull_request:
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -54,26 +56,64 @@ jobs:
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
           echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
+      - name: Make a cache directory for the container images
+        run: |
+          mkdir -p ./singularity_container_images
+
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core download ${{ env.REPO_LOWERCASE }} \
+          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
+      - name: Count the downloaded number of container images
+        id: count_initial
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Initial container image count: $image_count"
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test_stub,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test_stub,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
+            final_count=${{ env.IMAGE_COUNT_AFTER }}
+            difference=$((final_count - initial_count))
+            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi

.github/workflows/release-announcements.yml

@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         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' ' ')"  >> $GITHUB_OUTPUT
+          echo "topics=$(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
 
       - uses: rzr/fediverse-action@master
         with:

.github/workflows/template_version_comment.yml

@@ -0,0 +1,46 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Read template version from .nf-core.yml
+        uses: nichmor/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install nf-core
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Check nf-core outdated
+        id: nf_core_outdated
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          contains(env.OUTPUT, 'nf-core')
+        with:
+          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          allow-repeats: false
+          message: |
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+          #

.gitignore

@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/

.gitpod.yml

@@ -4,17 +4,14 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff

.nf-core.yml

@@ -1,4 +1,15 @@
 repository_type: pipeline
+nf_core_version: 3.0.2
+template:
+  author: Stephen Watts
+  description: A comprehensive cancer DNA/RNA analysis and reporting pipeline
+  force: false
+  is_nfcore: true
+  name: oncoanalyser
+  org: nf-core
+  outdir: .
+  skip_features: null
+  version: 1.1.0dev
 lint:
   actions_ci: False
   multiqc_config: False
@@ -10,6 +21,12 @@ lint:
     - params.max_cpus
     - params.max_memory
     - params.max_time
+  config_defaults:
+    - params.fastp_umi_length
+    - params.fastp_umi_skip
   files_unchanged: False
   actions_awsfulltest: False
 nf_core_version: "3.1.2"
+bump_version: null
+org_path: null
+update: null

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
           - [email protected]
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec

CHANGELOG.md

@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project mostly adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [dev]
+
+- [105](https://github.com/nf-core/oncoanalyser/pull/105) - Adjust MarkDups outputs to improve efficiency with k8s
+- [98](https://github.com/nf-core/oncoanalyser/pull/98) - Fix typos in error messages for process and run mode check
+- [96](https://github.com/nf-core/oncoanalyser/pull/96) - Added missing type field to an entry in the nextflow_schema.json
+- [95](https://github.com/nf-core/oncoanalyser/pull/95) - Post-release bump
+
 ## [[1.0.0](https://github.com/nf-core/oncoanalyser/releases/tag/1.0.0)] Pied Currawong - 2024-08-26
 
 Initial release of nf-core/oncoanalyser, created with the [nf-core](https://nf-co.re/) template.