Merge pull request #221 from nf-core/dev

Dev -> Master for v2.2 release

Author: drpatelh

.editorconfig

@@ -11,6 +11,9 @@ indent_style = space
 [*.{yml,yaml}]
 indent_size = 2
 
+[*.json]
+insert_final_newline = unset
+
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

.github/CONTRIBUTING.md

@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/viralrecon, the standard workflow i
     * If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/viralrecon repository](https://github.com/nf-core/viralrecon) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build .` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -69,12 +69,12 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
+5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
 6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
 7. Add sanity checks for all relevant parameters.
 8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
 9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yaml`.
+10. Add a new test command in `.github/workflow/ci.yml`.
 11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
 12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
 13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
@@ -83,7 +83,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
+Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -18,7 +18,7 @@ Please delete this text and anything that's not relevant from the template below
 I have checked the following places for your error:
 
 - [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-- [ ] [nf-core/viralrecon pipeline documentation](https://nf-co.re/nf-core/viralrecon/usage)
+- [ ] [nf-core/viralrecon pipeline documentation](https://nf-co.re/viralrecon/usage)
 
 ## Description of the bug
 
@@ -51,13 +51,12 @@ Have you provided the following extra information/files:
 
 ## Nextflow Installation
 
-- Version: <!-- [e.g. 19.10.0] -->
+- Version: <!-- [e.g. 21.04.0] -->
 
 ## Container engine
 
 - Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. nfcore/viralrecon:1.0.0] -->
 
 ## Additional context
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/vira
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
     - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](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](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/awsfulltest.yml

@@ -1,43 +1,33 @@
 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 can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   release:
     types: [published]
   workflow_dispatch:
-
-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 }}
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS full tests
     if: github.repository == 'nf-core/viralrecon'
     runs-on: ubuntu-latest
+    # Do a full-scale run with data from each sequencing platform
     strategy:
       matrix:
-        platform: ['illumina', 'nanopore']
+        platform: ["illumina", "nanopore"]
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
         with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        # Do a full-scale run with data from each sequencing platform
-        run: |
-          aws batch submit-job \
-            --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_'"${{matrix.platform}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"'/platform_'"${{matrix.platform}}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"'/'"${{matrix.platform}}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/viralrecon/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}"
+            }
+          profiles: '[ "test_full_${{ matrix.platform }}", "aws_tower" ]'

.github/workflows/awstest.yml

@@ -1,37 +1,27 @@
 name: nf-core AWS test
-# This workflow is triggered on push to the master branch.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
-# It runs the -profile 'test' on AWS batch.
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
 
 on:
   workflow_dispatch:
-
-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 }}
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS tests
     if: github.repository == 'nf-core/viralrecon'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
+
         with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        run: |
-          aws batch submit-job \
-          --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 --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"'"}]}'
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/viralrecon/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}"
+            }
+          profiles: '[ "test", "aws_tower" ]'

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: [21.04.0, ""]
+        nxf_ver: ["21.04.0", ""]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -111,7 +111,7 @@ jobs:
             --input false,
             --min_barcode_reads 10000,
             --min_guppyplex_reads 10000,
-            "--artic_minion_caller medaka",
+            "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false",
           ]
     steps:
       - name: Check out pipeline code

.github/workflows/linting.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-node@v1
         with:
-          node-version: "10"
+          node-version: '10'
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
@@ -35,7 +35,7 @@ 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`
+                * 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:
@@ -53,7 +53,7 @@ jobs:
 
       - uses: actions/setup-node@v1
         with:
-          node-version: "10"
+          node-version: '10'
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -67,7 +67,7 @@ jobs:
       - uses: actions/checkout@v1
       - uses: actions/setup-node@v1
         with:
-          node-version: "10"
+          node-version: '10'
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
@@ -101,6 +101,7 @@ jobs:
   nf-core:
     runs-on: ubuntu-latest
     steps:
+
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
@@ -113,8 +114,8 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: "3.6"
-          architecture: "x64"
+          python-version: '3.6'
+          architecture: 'x64'
 
       - name: Install dependencies
         run: |
@@ -126,7 +127,7 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
@@ -141,3 +142,4 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
+

.gitignore

@@ -3,7 +3,6 @@ work/
 data/
 results/
 .DS_Store
-tests/
 testing/
 testing*
 *.pyc