Merge pull request #1 from nf-cmgg/dev

Dev > main: first release

.editorconfig

@@ -28,6 +28,20 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
+[/assets/haplotype maps/*]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
+[/utils/nf-cmgg-sampletracking/*]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
 # ignore Readme
 [README.md]
 indent_style = unset

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,53 +2,53 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-- type: textarea
-  id: description
-  attributes:
-    label: Description of the bug
-    description: A clear and concise description of what the bug is.
-  validations:
-    required: true
-- type: textarea
-  id: command_used
-  attributes:
-    label: Command used and terminal output
-    description: Steps to reproduce the behaviour. Please paste the command you used
-      to launch the pipeline and the output from your terminal.
-    render: console
-    placeholder: '$ nextflow run ...
-
-
-      Some output where something broke
-
-      '
-- type: textarea
-  id: files
-  attributes:
-    label: Relevant files
-    description: 'Please drag and drop the relevant files here. Create a `.zip` archive
-      if the extension is not allowed.
-
-      Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-      in the directory where you launched the pipeline)_ as well as custom Nextflow
-      configuration files.
-
-      '
-- type: textarea
-  id: system
-  attributes:
-    label: System information
-    description: '* Nextflow version _(eg. 23.04.0)_
-
-      * Hardware _(eg. HPC, Desktop, Cloud)_
-
-      * Executor _(eg. slurm, local, awsbatch)_
-
-      * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
-      or Apptainer)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of nf-cmgg/sampletracking _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: "$ nextflow run ...
+
+
+        Some output where something broke
+
+        "
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
+
+        "
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: "* Nextflow version _(eg. 23.04.0)_
+
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+
+        * Executor _(eg. slurm, local, awsbatch)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
+
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
+        * Version of nf-cmgg/sampletracking _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.github/workflows/ci.yml

@@ -10,14 +10,18 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NFT_VER: "0.8.4"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     # 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-cmgg/sampletracking') }}"
     runs-on: ubuntu-latest
@@ -26,6 +30,10 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        tags:
+          - "workflows"
+        profile:
+          - "test,docker"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
@@ -38,9 +46,48 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml

.github/workflows/linting.yml

@@ -26,7 +26,7 @@ jobs:
         run: pip install pre-commit
 
       - name: Run pre-commit
-        run: pre-commit run --all-files
+        run: pre-commit run
 
   nf-core:
     runs-on: ubuntu-latest

.gitignore

@@ -6,3 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+.env
+.nf-test*

.nf-core.yml

@@ -1,24 +1,25 @@
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
   files_unchanged:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_dark.png
-  - .github/ISSUE_TEMPLATE/bug_report.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_dark.png
+    - .github/workflows/linting.yml
   multiqc_config:
-  - report_comment
+    - report_comment
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
+    - manifest.name
+    - manifest.homePage
 repository_type: pipeline
 template:
   prefix: nf-cmgg
-  skip: []
+  skip:
+    - igenomes