Important! Template update for nf-core/tools v2.3

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,4 +1,3 @@
-
 name: Bug report
 description: Report something that is broken or incorrect
 labels: bug

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/
     - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/mag _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/awsfulltest.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
+        uses: nf-core/tower-action@v3
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
@@ -31,4 +31,6 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mag/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
-          pre_run_script: 'export NXF_VER=21.10.3'
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/awstest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
+        uses: nf-core/tower-action@v3
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -25,4 +25,6 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mag/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-          pre_run_script: 'export NXF_VER=21.10.3'
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ env:
 
 jobs:
   test:
-    name: Run workflow tests
+    name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}
     runs-on: ubuntu-latest
@@ -47,4 +47,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

.github/workflows/linting.yml

@@ -12,9 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     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
       - name: Run Markdownlint
@@ -51,9 +49,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -64,14 +60,13 @@ jobs:
   YAML:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: 'Yamllint'
+        uses: karancode/yamllint-github-action@master
         with:
-          node-version: '10'
-      - name: Install yaml-lint
-        run: npm install -g yaml-lint
-      - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+          yamllint_file_or_dir: '.'
+          yamllint_config_filepath: '.yamllint.yml'
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -84,10 +79,11 @@ jobs:
             To keep the code consistent with lots of contributors, we run automated code consistency checks.
             To fix this CI test, please run:
 
-            * Install `yaml-lint`
-                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
+            * Install `yamllint`
+                * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint)
+                instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint)
             * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
                 * Fix any reported errors in your YAML files
 
             Once you push these changes the test should pass, and you can hide this comment :+1:

.gitpod.yml

@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore                 # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow                 # Highlight indentation level
+    - streetsidesoftware.code-spell-checker  # Spelling checker for source code

.nf-core.yml

@@ -0,0 +1 @@
+repository_type: pipeline

.yamllint.yml

@@ -0,0 +1,6 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable
+    truthy: disable

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.1.1 - [date]
+## v2.2.0dev - [date]
 
 Initial release of nf-core/mag, created with the [nf-core](https://nf-co.re/) template.
 

README.md

@@ -40,22 +40,22 @@ On release, automated continuous integration tests run the pipeline on a full-si
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run nf-core/mag -profile test,YOURPROFILE
+    nextflow run nf-core/mag -profile test,YOURPROFILE --outdir <OUTDIR>
     ```
 
     Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
 
     > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
     > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-    > * If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
+    > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
     > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
 
 4. Start running your own analysis!
 
     <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
     ```console
-    nextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --genome GRCh37
+    nextflow run nf-core/mag --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
 ## Documentation