Integrated bcellmagic and reveal

.devcontainer/devcontainer.json

@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // 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",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // 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"]
+        }
+    }
+}

.gitattributes

@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/airrflow/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 21.10.3)_
+        * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

.github/workflows/ci.yml

@@ -11,6 +11,10 @@ on:
 env:
   NXF_ANSI_LOG: false
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Run pipeline with test data
@@ -20,11 +24,28 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v4
+        with:
+          FILES: |
+            modules/local/airrflow_report/Dockerfile
+            modules/local/airrflow_report/environment.yml
+
+      - name: Build new docker image
+        if: env.MATCHED_FILES
+        run: docker build --no-cache . -t nfcore/airrflowreport:dev
+
+      - name: Pull docker image
+        if: ${{ !env.MATCHED_FILES }}
+        run: |
+          docker pull nfcore/airrflowreport:dev
+          docker tag nfcore/airrflowreport:dev nfcore/airrflowreport:dev
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -42,13 +63,83 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
+          - "latest-everything"
+        profile: ["test_tcr", "test_no_umi", "test_nocluster", "test_fetchimgt", "test_assembled"]
+      fail-fast: false
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v4
+        with:
+          FILES: |
+            modules/local/airrflow_report/Dockerfile
+            modules/local/airrflow_report/environment.yml
+
+      - name: Build new docker image
+        if: env.MATCHED_FILES
+        run: docker build --no-cache . -t nfcore/airrflowreport:dev
+
+      - name: Pull docker image
+        if: ${{ !env.MATCHED_FILES }}
+        run: |
+          docker pull nfcore/airrflowreport:dev
+          docker tag nfcore/airrflowreport:dev nfcore/airrflowreport:dev
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Run pipeline with test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}
+          path: |
+            /home/runner/.nextflow.log
+            /home/runner/work
+            !/home/runner/work/conda
+            !/home/runner/work/singularity
+
+  test_container:
+    name: Run workflow with immcantation devel test_container
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/airrflow') }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "22.10.1"
           - "latest-everything"
-        profile: ["test_tcr", "test_no_umi", "test_tcr_thr", "test_nocluster", "test_fetchimgt"]
+        profile: ["test_assembled_immcantation_devel", "test_raw_immcantation_devel"]
+      fail-fast: false
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v4
+        with:
+          FILES: |
+            modules/local/airrflow_report/Dockerfile
+            modules/local/airrflow_report/environment.yml
+
+      - name: Build new docker image
+        if: env.MATCHED_FILES
+        run: docker build --no-cache . -t nfcore/airrflowreport:dev
+
+      - name: Pull docker image
+        if: ${{ !env.MATCHED_FILES }}
+        run: |
+          docker pull nfcore/airrflowreport:dev
+          docker tag nfcore/airrflowreport:dev nfcore/airrflowreport:dev
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
@@ -57,3 +148,14 @@ jobs:
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}
+          path: |
+            /home/runner/.nextflow.log
+            /home/runner/work
+            !/home/runner/work/conda
+            !/home/runner/work/singularity

.github/workflows/fix-linting.yml

@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

.github/workflows/linting.yml

@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
   push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -12,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -25,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -38,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -69,12 +71,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.7"
           architecture: "x64"
@@ -97,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

.github/workflows/push_dockerhub_dev.yml

@@ -0,0 +1,28 @@
+name: nf-core Docker push (dev)
+# This builds the docker image and pushes it to DockerHub
+# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub (dev)
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/airrflow' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache ./modules/local/airrflow_report/ -t nfcore/airrflowreport:dev
+
+      - name: Push Docker image to DockerHub (dev)
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/airrflowreport:dev

.github/workflows/push_dockerhub_release.yml

@@ -0,0 +1,29 @@
+name: nf-core Docker push (release)
+# This builds the docker image and pushes it to DockerHub
+# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub (release)
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/airrflow' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache ./modules/local/airrflow_report/ -t nfcore/airrflowreport:latest
+
+      - name: Push Docker image to DockerHub (release)
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/airrflowreport:latest
+          docker tag nfcore/airrflowreport:latest nfcore/airrflowreport:${{ github.event.release.tag_name }}
+          docker push nfcore/airrflowreport:${{ github.event.release.tag_name }}

.nf-core.yml

@@ -1,5 +1,4 @@
 lint:
   files_exist:
     - conf/igenomes.config
-    - lib/WorkflowAirrflow.groovy
 repository_type: pipeline

.prettierignore

@@ -1,5 +1,6 @@
 email_template.html
 adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/
@@ -8,3 +9,4 @@ results/
 testing/
 testing*
 *.pyc
+bin/