Merge pull request #951 from nf-core/dev

Dev -> Master for v1.13.2 release

.github/RELEASE_CHECKLIST.md

@@ -2,13 +2,14 @@
 
 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where *Prefix* = *Metal* and *Dictionary* = *Animal*.
-3. Create a PR to `dev` to bump the version in  `CHANGELOG.md` and `setup.py`.
-4. Make sure all CI tests are passing!
-5. Create a PR from `dev` to `master`
-6. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
-7. Request review (2 approvals required)
-8. Merge the PR into `master`
-9. Once CI tests on commit have passed, create a new release copying the `CHANGELOG` for that release into the description section.
+3. Check whether the GitHub Actions workflow scripts need updating of the Nextflow versions
+4. Create a PR to `dev` to bump the version in  `CHANGELOG.md` and `setup.py`.
+5. Make sure all CI tests are passing!
+6. Create a PR from `dev` to `master`
+7. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
+8. Request review (2 approvals required)
+9. Merge the PR into `master`
+10. Once CI tests on commit have passed, create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 

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

@@ -4,6 +4,8 @@ on: [push, pull_request]
 jobs:
   MakeTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_VER: 21.03.0-edge
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -22,21 +24,32 @@ jobs:
         env:
           CAPSULE_LOG: none
         run: |
-          mkdir /tmp/nextflow
-          cd /tmp/nextflow
           wget -qO- get.nextflow.io | bash
-          sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+          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"
-          nf-core --log-file log.txt lint nf-core-testpipeline --fail-ignored
-          nf-core --log-file log.txt list
-          nf-core --log-file log.txt licences nf-core-testpipeline
-          nf-core --log-file log.txt sync nf-core-testpipeline/
-          nf-core --log-file log.txt schema build nf-core-testpipeline/ --no-prompts
-          nf-core --log-file log.txt bump-version nf-core-testpipeline/ 1.1
-          nf-core --log-file log.txt modules install nf-core-testpipeline/ --tool fastqc
+      - name: nf-core create
+        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
+
+      - 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 sync
+        run: nf-core --log-file log.txt sync nf-core-testpipeline/
+
+      - name: nf-core schema
+        run: nf-core --log-file log.txt schema build nf-core-testpipeline/ --no-prompts
+
+      - name: nf-core bump-version
+        run: nf-core --log-file log.txt bump-version nf-core-testpipeline/ 1.1
+
+      - name: nf-core modules install
+        run: nf-core --log-file log.txt modules install nf-core-testpipeline/ --tool fastqc
 
       - name: Upload log file artifact
         if: ${{ always() }}

.github/workflows/markdown-lint.yml

@@ -16,3 +16,29 @@ jobs:
 
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Markdown linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `markdownlint-cli`
+                * 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`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false

.github/workflows/pytest.yml

@@ -4,47 +4,46 @@ name: Python tests
 on:
   push:
     paths:
-      - '**.py'
+      - "**.py"
   pull_request:
     paths:
-      - '**.py'
+      - "**.py"
 
 jobs:
   pytest:
-
     runs-on: ubuntu-latest
+    env:
+      NXF_VER: 21.03.0-edge
     strategy:
       matrix:
         python-version: [3.6, 3.7, 3.8]
 
     steps:
-    - uses: actions/checkout@v2
-      name: Check out source-code repository
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Install python dependencies
-      run: |
-        python -m pip install --upgrade pip -r requirements-dev.txt
-        pip install -e .
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
 
-    - name: Install Nextflow
-      env:
+      - name: Install Nextflow
+        env:
           CAPSULE_LOG: none
-      run: |
-        mkdir /tmp/nextflow
-        cd /tmp/nextflow
-        wget -qO- get.nextflow.io | bash
-        sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
-
-    - name: Test with pytest
-      run: python3 -m pytest --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
-
-    - uses: codecov/codecov-action@v1
-      name: Upload code coverage report
-      with:
-        if: success()
-        token: ${{ secrets.CODECOV_TOKEN }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Test with pytest
+        run: python3 -m pytest --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
+
+      - uses: codecov/codecov-action@v1
+        name: Upload code coverage report
+        with:
+          if: success()
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/python-lint.yml

@@ -15,3 +15,25 @@ jobs:
 
       - name: Check code lints with Black
         uses: jpetrucciani/black-check@master
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false

.github/workflows/sync.yml

@@ -7,6 +7,8 @@ on:
 jobs:
   get-pipelines:
     runs-on: ubuntu-latest
+    env:
+      NXF_VER: 21.03.0-edge
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:

CHANGELOG.md

@@ -1,5 +1,15 @@
 # nf-core/tools: Changelog
 
+## [v1.13.2 - Copper Crocodile CPR :crocodile: :face_with_head_bandage:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-23]
+
+* Added better logging message if a user doesn't specificy the directory correctly with `nf-core modules` commands [[#942](https://github.com/nf-core/tools/pull/942)]
+* Fixed parameter validation bug caused by JSONObject [[#937](https://github.com/nf-core/tools/issues/937)]
+* Fixed template creation error regarding file permissions [[#932](https://github.com/nf-core/tools/issues/932)]
+* Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read
+* Added automated PR comments to the Markdown, YAML and Python lint CI tests to explain failures (tools and pipeline template)
+* Make `nf-core lint` summary table borders coloured according to overall pass / fail status
+* Attempted a fix for the automated sync when we submit too many PRs at once [[#911](https://github.com/nf-core/tools/issues/911)]
+
 ## [v1.13.1 - Copper Crocodile Patch :crocodile: :pirate_flag:](https://github.com/nf-core/tools/releases/tag/1.13.1) - [2021-03-19]
 
 * Fixed bug in pipeline linting markdown output that gets posted to PR comments [[#914]](https://github.com/nf-core/tools/issues/914)