Merge upstream changes, fix conflicts

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,42 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Hi there!
+
+        Thanks for telling us about a problem with the nf-core/tools package.
+
+  - 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 and output from your terminal.
+      render: console
+      placeholder: |
+        $ nf-core lint ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
+        * Python version _(eg. 3.7, 3.8)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,3 @@
-blank_issues_enabled: false
 contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for nf-core/tools
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/RELEASE_CHECKLIST.md

@@ -9,7 +9,9 @@
 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.
+10. Wait for CI tests on the commit to passed
+11. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
+12. Create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 

.github/workflows/build_gitpod.yml

@@ -0,0 +1,45 @@
+name: nf-core gitpod build and push
+# Builds the docker image for gitpod and pushes it to DockerHub
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'dev'
+    paths:
+      - 'nf_core/gitpod/gitpod.Dockerfile'
+      - '.github/workflows/build_gitpod.yml'
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/tools' }}
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASS  }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v3
+        with:
+          images: nfcore/gitpod
+          tags: |
+            type=semver,pattern={{version}}
+            type=raw,value=latest
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: nf_core/gitpod/gitpod.Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

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

@@ -1,12 +1,25 @@
 name: Create a pipeline and lint it
 on: [push, pull_request]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
+env:
+  NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
 
 jobs:
   MakeTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -23,7 +36,10 @@ jobs:
 
       - name: Install Nextflow
         env:
-          CAPSULE_LOG: none
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/

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

@@ -1,12 +1,25 @@
 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
+env:
+  NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
 
 jobs:
   RunTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -23,15 +36,18 @@ jobs:
 
       - name: Install Nextflow
         env:
-          CAPSULE_LOG: none
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         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
+          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

.github/workflows/markdown-lint.yml

@@ -7,9 +7,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
-        with:
-          node-version: "10"
+      - uses: actions/setup-node@v2
 
       - name: Install markdownlint
         run: npm install -g markdownlint-cli

.github/workflows/push_dockerhub_dev.yml

@@ -3,31 +3,27 @@ name: nf-core Docker push (dev)
 # Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
 on:
   push:
-    branches:
-      - dev
+    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/tools'}}
+    if: ${{ github.repository == 'nf-core/tools' }}
     env:
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
     strategy:
-      matrix:
-        image: [base, tools]
       fail-fast: false
     steps:
-      - name: Check out tools code
+      - name: Check out code
         uses: actions/checkout@v2
 
       - name: Build new docker image
-        run: docker build --no-cache . -t nfcore/${{ matrix.image }}:dev -f ${{ matrix.image }}.Dockerfile
+        run: docker build --no-cache . -t nfcore/tools:dev
 
       - name: Push Docker image to DockerHub (dev)
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/${{ matrix.image }}:dev
-
+          docker push nfcore/tools:dev

.github/workflows/push_dockerhub_release.yml

@@ -15,19 +15,17 @@ jobs:
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
     strategy:
-      matrix:
-        image: [base, tools]
       fail-fast: false
     steps:
       - name: Check out code
         uses: actions/checkout@v2
 
       - name: Build new docker image
-        run: docker build --no-cache . -t nfcore/${{ matrix.image }}:latest -f ${{ matrix.image }}.Dockerfile
+        run: docker build --no-cache . -t nfcore/tools:latest
 
       - name: Push Docker image to DockerHub (release)
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/${{ matrix.image }}:latest
-          docker tag nfcore/${{ matrix.image }}:latest nfcore/${{ matrix.image }}:${{ github.event.release.tag_name }}
-          docker push nfcore/${{ matrix.image }}:${{ github.event.release.tag_name }}
+          docker push nfcore/tools:latest
+          docker tag nfcore/tools:latest nfcore/tools:${{ github.event.release.tag_name }}
+          docker push nfcore/tools:${{ github.event.release.tag_name }}

.github/workflows/pytest.yml

@@ -3,11 +3,7 @@ name: Python tests
 # Only run if we changed a Python file
 on:
   push:
-    paths:
-      - "**.py"
   pull_request:
-    paths:
-      - "**.py"
 
 # Uncomment if we need an edge release of Nextflow again
 # env: NXF_EDGE: 1
@@ -17,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
 
     steps:
       - uses: actions/checkout@v2
@@ -41,7 +37,7 @@ jobs:
           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
+        run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
 
       - uses: codecov/codecov-action@v1
         name: Upload code coverage report

.github/workflows/python-lint.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Check code lints with Black
-        uses: jpetrucciani/black-check@master
+        uses: psf/black@stable
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment