Merge branch 'dev' into modules-create-type

.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

@@ -27,4 +27,3 @@ jobs:
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
           docker push nfcore/tools:dev
-

.github/workflows/tools-api-docs-release.yml

@@ -9,9 +9,9 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        dir: 
-            - latest
-            - ${{ github.event.release.tag_name }}
+        dir:
+          - latest
+          - ${{ github.event.release.tag_name }}
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v2

.github/workflows/yamllint.yml

@@ -0,0 +1,39 @@
+name: Lint YAML
+on: [push, pull_request]
+jobs:
+  YAML:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: 'Yamllint'
+        uses: karancode/yamllint-github-action@master
+        with:
+          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
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## YAML 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 `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") -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:
+
+            We highly recommend setting up yaml-lint 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

.gitpod.yml

@@ -1,17 +1,17 @@
 image: nfcore/gitpod:latest
 tasks:
   - name: install current state of nf-core/tools
-    command: |
-      python -m pip install --upgrade -r requirements-dev.txt -e .
+    command: python -m pip install --upgrade -r requirements-dev.txt -e .
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore                 # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
+    # - 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
+    # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow                 # Highlight indentation level
     - streetsidesoftware.code-spell-checker  # Spelling checker for source code
+    - DavidAnson.vscode-markdownlint         # Linter for markdown files

.yamllint.yml

@@ -0,0 +1,7 @@
+extends: default
+ignore: |
+    nf_core/*-template/
+rules:
+    document-start: disable
+    line-length: disable
+    truthy: disable

CHANGELOG.md

@@ -8,11 +8,25 @@
 * Replaced equals with ~ in nf-core headers, to stop false positive unresolved conflict errors when committing with VSCode.
 * Add retry strategy for AWS megatests after releasing [nf-core/tower-action v2.2](https://github.com/nf-core/tower-action/releases/tag/v2.2)
 * Added `.nf-core.yml` file with `repository_type: pipeline` for modules commands
+* Update igenomes path to the `BWAIndex` to fetch the whole `version0.6.0` folder instead of only the `genome.fa` file
+* Remove pinned Node version in the GitHub Actions workflows, to fix errors with `markdownlint`
+* Add yamllint GitHub Action.
+* Add `.yamllint.yml` to avoid line length and document start errors ([#1407](https://github.com/nf-core/tools/issues/1407))
+* Add `--publish_dir_mode` back into the pipeline template ([nf-core/rnaseq#752](https://github.com/nf-core/rnaseq/issues/752#issuecomment-1039451607))
 
 ## General
 
 * Updated `nf-core download` to work with latest DSL2 syntax for containers ([#1379](https://github.com/nf-core/tools/issues/1379))
 * Made `nf-core modules create` detect repository type with explicit `.nf-core.yml` or `--repo-type`, instead of random readme stuff ([#1391](https://github.com/nf-core/tools/pull/1391))
+* Added a Gitpod environment and Dockerfile ([#1384](https://github.com/nf-core/tools/pull/1384))
+    * Adds conda, Nextflow, nf-core, pytest-workflow, mamba, and pip to base Gitpod Docker image.
+    * Adds GH action to build and push Gitpod Docker image.
+    * Adds Gitpod environment to template.
+    * Adds Gitpod environment to tools with auto build of nf-core tool.
+* Shiny new command-line help formatting ([#1403](https://github.com/nf-core/tools/pull/1403))
+* Call the command line help with `-h` as well as `--help` (was formerly just the latter) ([#1404](https://github.com/nf-core/tools/pull/1404))
+* Add `.yamllint.yml` config file to avoid line length and document start errors in the tools repo itself.
+* Switch to `yamllint-github-action`to be able to configure yaml lint exceptions ([#1404](https://github.com/nf-core/tools/issues/1413))
 
 ### Modules
 
@@ -23,6 +37,8 @@
     * `input:` / `output:` not being specified in module
     * Allow for containers from other biocontainers resource as defined [here](https://github.com/nf-core/modules/blob/cde237e7cec07798e5754b72aeca44efe89fc6db/modules/cat/fastq/main.nf#L7-L8)
 * Fixed traceback when using `stageAs` syntax as defined [here](https://github.com/nf-core/modules/blob/cde237e7cec07798e5754b72aeca44efe89fc6db/modules/cat/fastq/main.nf#L11)
+* Allow conditional process execution from the configuration file ([#1393](https://github.com/nf-core/tools/pull/1393))
+* Add linting for when condition([#1397](https://github.com/nf-core/tools/pull/1397))
 
 ## [v2.2 - Lead Liger](https://github.com/nf-core/tools/releases/tag/2.2) - [2021-12-14]
 
@@ -65,11 +81,6 @@
 * Remove base `Dockerfile` used for DSL1 pipeline container builds
 * Run tests with Python 3.10
 * [#1363](https://github.com/nf-core/tools/pull/1363) Fix tools CI workflow nextflow versions.
-* [#1384](https://github.com/nf-core/tools/pull/1384) Adds Gitpod environment and Dockerfile.
-    * Adds conda, Nextflow, nf-core, pytest-workflow, mamba, and pip to base Gitpod Docker image.
-    * Adds GH action to build and push Gitpod Docker image.
-    * Adds Gitpod environment to template.
-    * Adds Gitpod environment to tools with auto build of nf-core tool.
 
 ### Modules