Try to move templating logic to make YAML files valid.

This means that we can run prettier directly on the entire codebase, without ignoring the template.
Will probably need quite a lot of sanity checking to make sure that I didn't break stuff!

.prettierignore

@@ -1,7 +1,3 @@
 docs/api/_build
 testing
 
-# Skip the templates as the Jinja2 tags confuse prettier
-# Don't worry - we run prettier on the compiled pipeline in create-lint-wf.yml
-nf_core/pipeline-template/
-nf_core/module-template/

nf_core/module-template/modules/meta.yml

@@ -1,27 +1,27 @@
-name: {{ tool_name_underscore }}
+name: "{{ tool_name_underscore }}"
 ## TODO nf-core: Add a description of the module and list keywords
 description: write your description here
 keywords:
   - sort
 tools:
-  - {{ tool }}:
+  - { { tool } }:
       ## TODO nf-core: Add a description and other details for the software below
-      description: {{ tool_description }}
-      homepage: {{ tool_doc_url }}
-      documentation: {{ tool_doc_url }}
-      tool_dev_url: {{ tool_dev_url }}
+      description: { { tool_description } }
+      homepage: { { tool_doc_url } }
+      documentation: { { tool_doc_url } }
+      tool_dev_url: { { tool_dev_url } }
       doi: ""
-      licence: {{ tool_licence }}
+      licence: { { tool_licence } }
 
 ## TODO nf-core: Add a description of all of the variables used as input
 input:
-  {% if has_meta -%}
+  #{% if has_meta %} Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  {% endif -%}
+  # {% endif %}
   ## TODO nf-core: Delete / customise this example input
   - bam:
       type: file
@@ -30,13 +30,13 @@ input:
 
 ## TODO nf-core: Add a description of all of the variables used as output
 output:
-  {% if has_meta -%}
+  #{% if has_meta -%} Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  {% endif -%}
+  # {% endif -%}
   - versions:
       type: file
       description: File containing software versions

nf_core/module-template/tests/test.yml

@@ -1,12 +1,12 @@
 ## TODO nf-core: Please run the following command to build this file:
 #                nf-core modules create-test-yml {{ tool }}{%- if subtool %}/{{ subtool }}{%- endif %}
-- name: {{ tool }}{{ ' '+subtool if subtool else '' }}
+- name: "{{ tool }}{{ ' '+subtool if subtool else '' }}"
   command: nextflow run ./tests/modules/{{ tool_dir }} -entry test_{{ tool_name_underscore }} -c ./tests/config/nextflow.config -c ./tests/modules/{{ tool_dir }}/nextflow.config
   tags:
-    - {{ tool }}
-    {%- if subtool %}
-    - {{ tool }}/{{ subtool }}
-    {%- endif %}
+    - "{{ tool }}"
+    # {%- if subtool %}
+    - "{{ tool }}/{{ subtool }}"
+    # {%- endif %}
   files:
-    - path: output/{{ tool }}/test.bam
+    - path: "output/{{ tool }}/test.bam"
       md5sum: e667c7caad0bc4b7ac383fd023c654fc

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -17,8 +17,7 @@ jobs:
         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
-        {%- raw %}
+        # on the `test_full.config` test runs with only one set of parameters {% raw %}
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

nf_core/pipeline-template/.github/workflows/awstest.yml

@@ -10,9 +10,9 @@ jobs:
     if: github.repository == '{{ name }}'
     runs-on: ubuntu-latest
     steps:
+      # Launch workflow using Tower CLI tool action {%- raw %}
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        {%- raw %}
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

nf_core/pipeline-template/.github/workflows/branch.yml

@@ -5,17 +5,19 @@ on:
   pull_request_target:
     branches: [master]
 
+env:
+  REPO_NAME: "{{ name }}"
+
 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
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches. {% raw %}
       - name: Check PRs
-        if: github.repository == '{{ name }}'
+        if: github.repository == env.REPO_NAME
         run: |
-          { [[ {% raw %}${{github.event.pull_request.head.repo.full_name }}{% endraw %} == {{ name }} ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == env.REPO_NAME ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
-{%- raw %}
       # 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
@@ -43,4 +45,3 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-{%- endraw %}

nf_core/pipeline-template/.github/workflows/ci.yml

@@ -11,12 +11,13 @@ on:
 env:
   NXF_ANSI_LOG: false
   CAPSULE_LOG: none
+  REPO_NAME: "{{ name }}"
 
 jobs:
   test:
     name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: {% raw %}${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}{% endraw %}
+    # Only run on push if this is the nf-core dev branch (merged PRs) {% raw %}
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == env.REPO_NAME) }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -34,12 +35,10 @@ jobs:
 
       - name: Install Nextflow
         env:
-          {% raw -%}
           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 }}
-          {%- endraw %}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -1,14 +1,14 @@
-{% raw %}name: nf-core linting
+name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+# It runs the `nf-core lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines. {% raw %}
 on:
   push:
   pull_request:
   release:
     types: [published]
 
 jobs:
-
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
@@ -78,4 +78,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-{%- endraw %}

nf_core/pipeline-template/.github/workflows/linting_comment.yml

@@ -1,7 +1,6 @@
-{% raw -%}
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
-# It posts an automated comment to the PR, even if the PR is coming from a fork
+# It posts an automated comment to the PR, even if the PR is coming from a fork {% raw -%}
 
 on:
   workflow_run:
@@ -27,4 +26,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-{%- endraw %}

nf_core/pipeline-template/assets/multiqc_config.yaml

@@ -5,7 +5,7 @@ report_comment: >
 report_section_order:
   software_versions:
     order: -1000
-  {{ name.lower().replace('/', '-') }}-summary:
+  "{{ name.lower().replace('/', '-') }}-summary":
     order: -1001
 
 export_plots: true