Merge pull request #1183 from nf-core/dev

Dev -> Master for v2.0 release

.github/workflows/create-lint-wf.yml

@@ -32,28 +32,28 @@ jobs:
         run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
       - name: nf-core lint
-        run: nf-core --log-file log.txt lint nf-core-testpipeline --fail-ignored
+        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored
 
       - name: nf-core list
         run: nf-core --log-file log.txt list
 
-      - name: nf-core licences
-        run: nf-core --log-file log.txt licences nf-core-testpipeline
+      # - name: nf-core licences
+      #   run: nf-core --log-file log.txt licences nf-core-testpipeline
 
       - name: nf-core sync
-        run: nf-core --log-file log.txt sync nf-core-testpipeline/
+        run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
 
       - name: nf-core schema
-        run: nf-core --log-file log.txt schema build nf-core-testpipeline/ --no-prompts
+        run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
 
       - name: nf-core bump-version
-        run: nf-core --log-file log.txt bump-version nf-core-testpipeline/ 1.1
+        run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
 
       - name: nf-core lint in release mode
-        run: nf-core --log-file log.txt lint nf-core-testpipeline --fail-ignored --release
+        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --release
 
       - name: nf-core modules install
-        run: nf-core --log-file log.txt modules install nf-core-testpipeline/ --tool fastqc
+        run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force --latest
 
       - name: Upload log file artifact
         if: ${{ always() }}

.github/workflows/create-test-wf.yml

@@ -0,0 +1,41 @@
+name: Create a pipeline and test it
+on: [push, pull_request]
+
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
+jobs:
+  RunTestWorkflow:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run nf-core/tools
+        run: |
+          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+          nextflow run nf-core-testpipeline -profile test,docker
+
+      - name: Upload log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: nf-core-log-file
+          path: log.txt

.github/workflows/markdown-lint.yml

@@ -9,13 +9,13 @@ jobs:
 
       - uses: actions/setup-node@v1
         with:
-          node-version: '10'
+          node-version: "10"
 
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
 
       - name: Run Markdownlint
-        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+        run: markdownlint .
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -32,8 +32,8 @@ jobs:
                 * On Mac: `brew install markdownlint-cli`
                 * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
             * Fix the markdown errors
-                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
-                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
+                * Automatically: `markdownlint . --fix`
+                * Manually resolve anything left from `markdownlint .`
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
 

.github/workflows/push_dockerhub_dev.yml

@@ -18,6 +18,7 @@ jobs:
     strategy:
       matrix:
         image: [base, tools]
+      fail-fast: false
     steps:
       - name: Check out tools code
         uses: actions/checkout@v2

.github/workflows/push_dockerhub_release.yml

@@ -17,6 +17,7 @@ jobs:
     strategy:
       matrix:
         image: [base, tools]
+      fail-fast: false
     steps:
       - name: Check out code
         uses: actions/checkout@v2
@@ -28,5 +29,5 @@ jobs:
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
           docker push nfcore/${{ matrix.image }}:latest
-          docker tag nfcore/${{ matrix.image }}:latest nf-core/${{ matrix.image }}:${{ github.event.release.tag_name }}
+          docker tag nfcore/${{ matrix.image }}:latest nfcore/${{ matrix.image }}:${{ github.event.release.tag_name }}
           docker push nfcore/${{ matrix.image }}:${{ github.event.release.tag_name }}

.github/workflows/tools-api-docs-release.yml

@@ -9,8 +9,9 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        dir: [latest, $GITHUB_REF]
-
+        dir: 
+            - latest
+            - ${{ github.event.release.tag_name }}
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v2

.github/markdownlint.yml → .markdownlint.yml

@@ -1,6 +1,8 @@
 # Markdownlint configuration file
 default: true
 line-length: false
+ul-indent:
+    indent: 4
 no-duplicate-header:
     siblings_only: true
 no-inline-html:
@@ -10,7 +12,6 @@ no-inline-html:
         - kbd
         - details
         - summary
-        - kbd
 # tools only - the {{ jinja variables }} break URLs and cause this to error
 no-bare-urls: false
 # tools only - suppresses error messages for usage of $ in main README