Merge branch 'dev' of https://github.com/nf-core/viralrecon into dev

.github/.dockstore.yml

@@ -0,0 +1,5 @@
+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config

.github/CONTRIBUTING.md

@@ -46,12 +46,12 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Patch
 
-: warning: Only in the unlikely and regretful event of a release happening with a bug.
+:warning: Only in the unlikely and regretful event of a release happening with a bug.
 
 * On your own fork, make a new branch `patch` based on `upstream/master`.
 * Fix the bug, and bump version (X.Y.Z+1).
 * A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/viralrecon documentation](https://nf-co.re/nf-core/viralrecon/docs) and don't hesitate to get in touch on the nf-core Slack [#viralrecon](https://nfcore.slack.com/channels/viralrecon) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/viralrecon documentation](https://nf-co.re/viralrecon/usage) and don't hesitate to get in touch on the nf-core Slack [#viralrecon](https://nfcore.slack.com/channels/viralrecon) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,24 +1,32 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
+<!--
 # nf-core/viralrecon bug report
 
 Hi there!
 
 Thanks for telling us about a problem with the pipeline.
 Please delete this text and anything that's not relevant from the template below:
+-->
 
-## Describe the bug
+## Description of the bug
 
-A clear and concise description of what the bug is.
+<!-- A clear and concise description of what the bug is. -->
 
 ## Steps to reproduce
 
 Steps to reproduce the behaviour:
 
-1. Command line: `nextflow run ...`
-2. See error: _Please provide your error message_
+1. Command line: <!-- [e.g. `nextflow run ...`] -->
+2. See error: <!-- [Please provide your error message] -->
 
 ## Expected behaviour
 
-A clear and concise description of what you expected to happen.
+<!-- A clear and concise description of what you expected to happen. -->
 
 ## System
 
@@ -33,10 +41,10 @@ A clear and concise description of what you expected to happen.
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/viralrecon:1.0.0] -->
 
 ## Additional context
 
-Add any other context about the problem here.
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #viralrecon channel"
+    url: https://nfcore.slack.com/channels/viralrecon
+    about: Discussion about the nf-core/viralrecon pipeline

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,24 +1,32 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core website
+labels: enhancement
+---
+
+<!--
 # nf-core/viralrecon feature request
 
 Hi there!
 
 Thanks for suggesting a new feature for the pipeline!
 Please delete this text and anything that's not relevant from the template below:
+-->
 
 ## Is your feature request related to a problem? Please describe
 
-A clear and concise description of what the problem is.
+<!-- A clear and concise description of what the problem is. -->
 
-Ex. I'm always frustrated when [...]
+<!-- e.g. [I'm always frustrated when ...] -->
 
 ## Describe the solution you'd like
 
-A clear and concise description of what you want to happen.
+<!-- A clear and concise description of what you want to happen. -->
 
 ## Describe alternatives you've considered
 
-A clear and concise description of any alternative solutions or features you've considered.
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
 
 ## Additional context
 
-Add any other context about the feature request here.
+<!-- Add any other context about the feature request here. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,19 +1,20 @@
+<!--
 # nf-core/viralrecon pull request
 
 Many thanks for contributing to nf-core/viralrecon!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md)
+-->
+
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason)
+- [ ] `CHANGELOG.md` is updated
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If necessary, also make a PR on the [nf-core/viralrecon branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/viralrecon)
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
-- [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Documentation in `docs` is updated
-- [ ] `CHANGELOG.md` is updated
-- [ ] `README.md` is updated
-
-**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the [nf-core/viralrecon branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/viralrecon)

.github/markdownlint.yml

@@ -5,5 +5,3 @@ no-duplicate-header:
     siblings_only: true
 MD033:
     allowed_elements: [details, summary, p, img]
-MD007:
-    indent: 4

.github/workflows/awsfulltest.yml

@@ -1,36 +1,39 @@
-name: nf-core AWS full test
-# This workflow is triggered on releases.
+name: nf-core AWS full size tests
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  workflow_run:
+    workflows: ["nf-core Docker push (release)"]
+    types: [completed]
+  workflow_dispatch:
 
 jobs:
   run-awstest:
+    name: Run AWS full tests
     if: github.repository == 'nf-core/viralrecon'
-    name: Run AWS test
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
       - name: Install awscli
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
         env:
-          AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
-          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
-          TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
-          #AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
-          AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
-          AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
-        run: | # Submits job to AWS batch using a 'nextflow-4GiB' job definition. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files.
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+        run: |
           aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-viralrecon \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition nextflow-4GiB \
-          --container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}'
+            --region eu-west-1 \
+            --job-name nf-core-viralrecon \
+            --job-queue $AWS_JOB_QUEUE \
+            --job-definition $AWS_JOB_DEFINITION \
+            --container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/awstest.yml

@@ -1,37 +1,36 @@
 name: nf-core AWS test
 # This workflow is triggered on push to the master branch.
-# It runs the -profile 'test' on AWS batch
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
-      - dev # only for testing purposes, to be removed
+  workflow_dispatch:
+
 jobs:
   run-awstest:
+    name: Run AWS tests
     if: github.repository == 'nf-core/viralrecon'
-    name: Run AWS test
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
       - name: Install awscli
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
         env:
-          AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
-          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
-          TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
-          #AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
-          AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
-          AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
-        run: | # Submits job to AWS batch using a 'nextflow-4GiB' job definition. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files.
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+        run: |
           aws batch submit-job \
           --region eu-west-1 \
           --job-name nf-core-viralrecon \
           --job-queue $AWS_JOB_QUEUE \
-          --job-definition nextflow-4GiB \
-          --container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}'
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/branch.yml

@@ -1,16 +1,36 @@
-name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
-on:
-  pull_request:
-    branches:
-    - master
-
-jobs:
-  test:
-    runs-on: ubuntu-18.04
-    steps:
-      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
-      - name: Check PRs
-        run: |
-          { [[ $(git remote get-url origin) == *nf-core/viralrecon ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
+name: nf-core branch protection
+# This workflow is triggered on PRs to master branch on the repository
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+on:
+  pull_request_target:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      - name: Check PRs
+        if: github.repository == 'nf-core/viralrecon'
+        run: |
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/viralrecon ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            The `master` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+
+            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false