Merge pull request #3108 from mirpedrol/template-customisation-yaml-file

Template: handle template features with a yaml file
nf-core · Aug 13, 2024 · 90f963c · 90f963c
2 parents ef946e9 + 6af86cf
commit 90f963c
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diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -31,33 +31,41 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
+  prepare-matrix:
+    name: Retrieve all template features
+    runs-on: ubuntu-latest
+    outputs:
+      all_features: ${{ steps.create_matrix.outputs.matrix }}
+    steps:
+      - name: 🏗 Set up yq
+        uses: frenck/action-setup-yq@v1
+      - name: checkout
+        uses: actions/checkout@v3
+      - name: Create Matrix
+        id: create_matrix
+        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print $2}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT
+
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
     env:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        TEMPLATE:
-          - "template_skip_github_badges.yml"
-          - "template_skip_igenomes.yml"
-          - "template_skip_ci.yml"
-          - "template_skip_code_linters.yml"
-          - "template_skip_citations.yml"
-          - "template_skip_gitpod.yml"
-          - "template_skip_codespaces.yml"
-          - "template_skip_multiqc.yml"
-          - "template_skip_changelog.yml"
+        TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }}
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
         profile: ["self_hosted_runner"]
         include:
-          - TEMPLATE: "template_skip_all.yml"
+          - TEMPLATE: all
             runner: ubuntu-latest
             profile: "docker"
-          - TEMPLATE: "template_skip_nf_core_configs.yml"
+          - TEMPLATE: nf_core_configs
             runner: ubuntu-latest
             profile: "docker"
+        exclude:
+          - TEMPLATE: github
+          - TEMPLATE: is_nfcore
       fail-fast: false
 
     steps:
@@ -90,53 +98,17 @@ jobs:
         run: |
           mkdir create-test-lint-wf
           export NXF_WORK=$(pwd)
-          printf "org: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
-
-      - name: Create template skip github_badges
-        run: |
-          printf "org: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
-
-      - name: Create template skip igenomes
-        run: |
-          printf "org: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
-
-      - name: Create template skip ci
-        run: |
-          printf "org: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
-
-      - name: Create template skip nf_core_configs
-        run: |
-          printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
-
-      - name: Create template skip code_linters
-        run: |
-          printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
-
-      - name: Create template skip citations
-        run: |
-          printf "org: my-prefix\nskip: citations" > create-test-lint-wf/template_skip_citations.yml
-
-      - name: Create template skip gitpod
-        run: |
-          printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml
-
-      - name: Create template skip multiqc
-        run: |
-          printf "org: my-prefix\nskip: multiqc" > create-test-lint-wf/template_skip_multiqc.yml
-
-      - name: Create template skip changelog
-        run: |
-          printf "org: my-prefix\nskip: changelog" > create-test-lint-wf/template_skip_changelog.yml
+          printf "org: my-prefix\nskip: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
 
-      - name: Create template skip codespaces
+      - name: Create template skip {{ matrix.TEMPLATE }}
         run: |
-          printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml
+          printf "org: my-prefix\nskip: {{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
           cd create-test-lint-wf
-          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml
 
       - name: run the pipeline
         run: |

diff --git a/.prettierignore b/.prettierignore
@@ -7,6 +7,7 @@ nf_core/module-template/meta.yml
 nf_core/pipeline-template/nextflow_schema.json
 nf_core/pipeline-template/modules.json
 nf_core/pipeline-template/tower.yml
+tests/data/pipeline_create_template_skip.yml
 # don't run on things handled by ruff
 *.py
 *.pyc

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@
 - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105))
 - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
+- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
 
 ### Linting
 

diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py
@@ -1,11 +1,14 @@
 """A Textual app to create a pipeline."""
 
 import logging
+from pathlib import Path
 
 import click
+import yaml
 from textual.app import App
 from textual.widgets import Button
 
+import nf_core
 from nf_core.pipelines.create import utils
 from nf_core.pipelines.create.basicdetails import BasicDetails
 from nf_core.pipelines.create.custompipeline import CustomPipeline
@@ -68,6 +71,9 @@ class PipelineCreateApp(App[utils.CreateConfig]):
     # Logging state
     LOGGING_STATE = None
 
+    # Template features
+    template_features_yml = utils.load_features_yaml()
+
     def on_mount(self) -> None:
         self.push_screen("welcome")